EGAD00000000001
WTCCC1 project samples from 1958 British Birth Cohort
Affymetrix 500K
1504
EGAD00000000002
WTCCC1 project samples from UK National Blood Service
Affymetrix 500K
1500
EGAD00000000003
WTCCC1 project Bipolar Disorder (BD) samples
1
EGAD00000000004
WTCCC1 project Coronary Artery Disease (CAD) samples
1
EGAD00000000005
WTCCC1 project Inflammatory Bowel Disease (IBD) samples
1
EGAD00000000006
WTCCC1 project Hypertension (HT) samples
1
EGAD00000000007
WTCCC1 project Rheumatooid arthritis (RA) samples
1
EGAD00000000008
WTCCC1 project Type 1 Diabetes (T1D) samples
1
EGAD00000000009
WTCCC1 project Type 2 Diabetes (T2D) samples
1
EGAD00000000010
WTCCC1 project Ankylosing Spondylitis (AS) samples
Illumina 15K
957
EGAD00000000011
WTCCC1 project Autoimmune Thyroid Disease (ATD) samples
Illumina 15K
900
EGAD00000000012
WTCCC1 project Multiple Sclerosis (MS) samples
975
EGAD00000000013
WTCCC1 project Breast cancer (BC) samples
Illumina 15K
1004
EGAD00000000014
WTCCC1 project samples from 1958 British Birth Cohort
1504
EGAD00000000015
WTCCC project African control samples
Affymetrix 500K
1496
EGAD00000000016
WTCCC project Tuberculosis (TB) samples
Affymetrix 500K
1498
EGAD00000000017
Cord blood control samples from Gambia
-
EGAD00000000018
Severe malaria cases from Gambia
-
EGAD00000000019
840 families where both parents have been genotyped together with the child with severe malaria
1
EGAD00000000020
685 families where both parents have been genotyped together with the child with severe malaria
-
EGAD00000000021
WTCCC2 project samples from 1958 British Birth Cohort
3000
EGAD00000000022
WTCCC2 project samples from 1958 British Birth Cohort
3000
EGAD00000000023
WTCCC2 project samples from National Blood Donors (NBS) Cohort
1
EGAD00000000024
WTCCC2 project samples from National Blood Donors (NBS) Cohort
1
EGAD00000000025
WTCCC2 project Ulcerative Colitis (UC) samples
Affymetrix 6.0
2869
EGAD00000000026
Randomly-selected, unrelated individuals
Illumina 610-Quad
518
EGAD00000000027
eQTL data for European newborns
Ilumina HumanHap550-2v3_B-Beadstudio
176
EGAD00000000028
Aggregate results from a GWAS study on 3352 cases abd 3145 controls
6497
EGAD00000000029
Aggregate results from a case-control study on stroke and ischemic stroke.
19602
EGAD00000000030
T1DGC project 1958 British Birth Cohort samples
2604
EGAD00000000031
HLA genotyping of 1958 British Birth Cohort samples
1
EGAD00000000032
NcOEDG Helsinki 1 samples
1
EGAD00000000033
NcOEDG Helsinki 2 samples
1
EGAD00000000034
NcOEDG Helsinki 3 samples
1
EGAD00000000035
NcOEDG Helsinki 4 samples
1
EGAD00000000036
NcOEDG Stockholm 1 samples
1
EGAD00000000037
NcOEDG Stockholm 2 samples
1
EGAD00000000038
NcOEDG Stockholm 3 samples
1
EGAD00000000039
NcOEDG Malmo - Lund samples
1
EGAD00000000040
GenomEUtwin Danish (DK) samples
1
EGAD00000000041
GenomEUtwin Swedish (SWE) samples
1
EGAD00000000042
GenomEUtwin Finnish (FIN) samples
1
EGAD00000000043
GenomeEUtwin control samples
Illumina HumanHap300-Duo
Illumina HumanHap 550K
2099
EGAD00000000044
Northern Finland Birth Cohort 1966 samples
Illumina HumanHap370
5844
EGAD00000000045
Genomic sequencing and transcriptome shotgun sequencing of a metastatic tumour and its recurrence after drug therapy in a single patient
Illumina Genome Analyzer II
1
EGAD00000000046
RNA-SEQ data from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples
4
EGAD00000000047
Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples
4
EGAD00000000048
Sequencing data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample
Illumina Genome Analyzer II
1
EGAD00000000049
RNA-SEQ data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample
Illumina Genome Analyzer II
1
EGAD00000000051
Sequencing data from matching Renal Carcinoma samples
Illumina Genome Analyzer II
25
EGAD00000000052
Sequencing data from natching Pancreatic Carcinoma samples
Illumina Genome Analyzer II
25
EGAD00000000053
Sequencing data from Breast Cancer samples
Illumina Genome Analyzer II
1
EGAD00000000054
NCI-H209 is an immortal cell line derived from a bone marrow metastasis of a patient with small cell lung cancer, taken before chemotherapy. The specimen showed histologically typical small cells with classic neuroendocrine features. NCI-BL209 is an EBV-transformed B-cell line derived from the same patient as the small cell lung cancer cell line, NCI-H209
Life Tech - Solid
1
EGAD00000000055
COLO-829 is a publicly available immortal cancer cell line and COLO-829BL is a lymphoblastoid cell line derived from the same patient
Illumina Genome Analyzer II
2
EGAD00000000056
WTCCC project samples from the primary biliary cirrhosis cohort
Illumina 610K Quad
1705
EGAD00000000057
WTCCC project samples from the Parkinson's disase cohort
Illumina 610K Quad
1705
EGAD00000000058
Aggregate results from 22 Carbamazepine-induced hypersensitivity syndrome patients and 2691 UK National Blood Service (NBS) control samples
2713
EGAD00000000059
Aggregate results from 43 Carbamazepine-induced hypersensitivity syndrome patients and 1296 1958 British Birth Cohort control samples
1
EGAD00000000060
Samples from the UK Glomerulonephritis DNA bank
-
EGAD00000000073
Gabriel samples from the 1958 British Birth Cohort
1
EGAD00000000074
Gabriel samples from the Swedish BAMSE Cohort
1
EGAD00000000075
Gabriel samples from the Swedish BAMSE Cohort
1
EGAD00000000076
Gabriel samples from the Australian Bussleton Cohort
1
EGAD00000000077
Gabriel samples from the Australian Bussleton Cohort
1
EGAD00000000082
Gabriel samples from the French EGEA Cohort
1
EGAD00000000083
Gabriel samples from the French EGEA Cohort
1
EGAD00000000084
Gabriel samples from the German Gabriel Advanced Survey
1
EGAD00000000085
Gabriel samples from the German Gabriel Advanced Survey
1
EGAD00000000086
Gabriel samples from the multicenter GAIN cohort
1
EGAD00000000087
Gabriel samples from the multicenter GAIN cohort
1
EGAD00000000088
Gabriel samples from the Karelia Allergy Study
1
EGAD00000000089
Gabriel samples from the Karelia Allergy Study
1
EGAD00000000090
Gabriel samples from the Russian KMSU cohort
1
EGAD00000000091
Gabriel samples from the Russian KMSU cohort
1
EGAD00000000092
Gabriel samples from the German MAGIS cohort
1
EGAD00000000093
Gabriel samples from the German MAGIS cohort
1
EGAD00000000094
Gabriel samples from the UK MRCA cohort
1
EGAD00000000101
Gabriel samples from the Russian TOMSK cohort
1
EGAD00000000102
Gabriel samples from the Russian TOMSK cohort
1
EGAD00000000103
Gabriel samples from the Russian UFA cohort
1
EGAD00000000104
Gabriel samples from the Russian UFA cohort
1
EGAD00000000105
Gabriel samples from the multicenter occupational cohort
1
EGAD00000000106
Gabriel samples from the multicenter occupational cohort
1
EGAD00000000107
Gabriel samples from the multicenter occupational cohort
1
EGAD00000000108
Gabriel samples from the UK AUGOSA cohort
1
EGAD00000000109
Gabriel samples from the UK SEVERE cohort
1
EGAD00000000114
Whole transcriptome sequence data from 18 ovarian clear-cell carcinoma samples and one TOV21G ovarian clear-cell carcinoma cell line
Illumina Genome Analyzer II
1
EGAD00000000115
Summary data from GWAS analysis on 856 cases and 2836 control
3719
EGAD00000000119
Genotypes from cell lines derived from breast carcinoma tissue
Affymetrix 6.0
51
EGAD00000000120
WTCCC2 project Multiple Sclerosis (MS) samples
Human670-QuadCustom v1
11375
EGAD00000000121
Genotypes at MITF E318K variant
Taqman and sequencing
2488
EGAD00000000122
Genotypes at MITF E318K variant
Illumina Human660W-Quad
Illumina HumanCNV370
Illumina HumanHap 300 v2 Duo
1925
EGAD00001000001
Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma
Illumina Genome Analyzer II
18
EGAD00001000002
Massive genomic rearrangement acquired in a single catastrophic event during cancer development
Illumina Genome Analyzer
Illumina Genome Analyzer II
11
EGAD00001000003
Gencode Exome Pilot
Illumina Genome Analyzer II
7
EGAD00001000004
CLL cancer Sample Sequencing
Illumina Genome Analyzer
Illumina Genome Analyzer II
5
EGAD00001000005
Various Cancer Fusion Gene Sequencing
Illumina Genome Analyzer II
14
EGAD00001000007
Osteosarcoma Sequencing
Illumina Genome Analyzer II
43
EGAD00001000013
CLL Cancer Whole Genome Sequencing
Illumina Genome Analyzer II
19
EGAD00001000014
Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.
Illumina Genome Analyzer II
54
EGAD00001000015
Exome sequencing of hyperplastic polyposis patients.
Illumina Genome Analyzer II
Illumina HiSeq 2000
84
EGAD00001000016
Familial Melanoma Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
89
EGAD00001000017
PAS Pedigrees: Identification of novel genetic variants contributing to cardiovascular disease in pedigrees with premature atherosclerosis.
Illumina Genome Analyzer II
Illumina HiSeq 2000
18
EGAD00001000018
Identifying causative mutations for Thrombocytopenia with Absent Radii
Illumina Genome Analyzer II
5
EGAD00001000019
Lethal malformation syndrome
Illumina Genome Analyzer II
6
EGAD00001000021
Paroxysmal neurological disorders
Illumina Genome Analyzer II
Illumina HiSeq 2000
97
EGAD00001000022
Exome sequencing in patients with cardiac arrhythmias
Illumina Genome Analyzer II
20
EGAD00001000023
Recurrent Somatic Mutations in CLL
Illumina Genome Analyzer IIx
11
EGAD00001000024
Whole Exome Sequencing for Characterization of Disease Causing Mutations in two Pakistani Families Suffering from Autosomal Recessive Ocular Disorders.
Illumina Genome Analyzer II
4
EGAD00001000025
Determination of the molecular nature of the Vel blood group by exome sequencing
Illumina Genome Analyzer II
4
EGAD00001000026
Investigation of the genetic basis of the rare syndrome Post-Transfusion Purpura (PTP)
Illumina Genome Analyzer II
5
EGAD00001000027
ICGC Germany PedBrain Medulloblastoma Pilot_2_LM
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
8
EGAD00001000029
Grey Platelet Syndrome (GPS)
Illumina Genome Analyzer II
5
EGAD00001000030
Analysis of genomic integrity of disease-corrected human induced pluripotent stem cells by exome sequencing
Illumina HiSeq 2000
4
EGAD00001000031
Human Colorectal Cancer Exome Sequencing
Illumina Genome Analyzer II
16
EGAD00001000032
Hepatitis C IL28B pooled resequencing study with 100 responders and 100 non-responders
Illumina Genome Analyzer IIx
4
EGAD00001000033
"SNV detection from formalin fixed paraffin embedded (FFPE) samples"
Illumina Genome Analyzer II
6
EGAD00001000034
"Usage of small amounts of DNA for Illumina sequencing"
Illumina Genome Analyzer II
3
EGAD00001000035
"Single nucleotide variant detection in multiple foci of three prostate cancer tumors"
Illumina Genome Analyzer II
9
EGAD00001000036
"Copy number variant detection in multiple foci of three prostate cancer tumors"
Illumina Genome Analyzer II
9
EGAD00001000037
An evaluation of different strategies for large-scale pooled sequencing study design.
Illumina Genome Analyzer II
7
EGAD00001000038
Hyperfibrinolysis
Illumina Genome Analyzer II
5
EGAD00001000039
Platelet collagen defect
Illumina Genome Analyzer II
Illumina HiSeq 2000
11
EGAD00001000040
Bleeding
Illumina Genome Analyzer II
6
EGAD00001000041
Various Platelet Disorders
Illumina Genome Analyzer II
7
EGAD00001000042
Whole-Exome-Seq-Dataset
Illumina Genome Analyzer IIx
30
EGAD00001000043
RNA-Seq-Dataset
Illumina Genome Analyzer IIx
16
EGAD00001000044
Recurrent Somatic Mutations in CLL
Illumina Genome Analyzer IIx
212
EGAD00001000045
Somatic mutation of SF3B1 in myelodysplasia with ring sideroblasts and other cancers
Illumina Genome Analyzer II
Illumina HiSeq 2000
33
EGAD00001000046
Gastric Cancer Exome Sequencing
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
43
EGAD00001000047
exome sequence data for 49 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000087) of raw BAMs mapped to GRCh37_53.
Illumina HiSeq 2000
49
EGAD00001000048
monozygotic twin discordant for schizophrenia
Complete Genomics
2
EGAD00001000049
Pancreatic adenocarcinoma QCMG 20110901
AB SOLiD 4 System
AB SOLiD System 3.0
26
EGAD00001000050
Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes
Illumina Genome Analyzer II
13
EGAD00001000052
UK10K_NEURO_MUIR REL-2011-01-28
Illumina Genome Analyzer II
104
EGAD00001000053
Exome sequencing in patients with Calcific Aortic Valve Stenosis
Illumina HiSeq 2000
20
EGAD00001000054
Mutational Screening of Human Acute Myleloid Leukaemia Samples
Illumina HiSeq 2000
10
EGAD00001000055
Genetic variation in Kuusamo
Illumina HiSeq 2000
434
EGAD00001000057
RNA-Seq analysis
Illumina Genome Analyzer II
15
EGAD00001000058
Exome Sequencing analysis
Illumina Genome Analyzer II
21
EGAD00001000059
Screening for human epigenetic variation at CpG islands
Illumina Genome Analyzer II
116
EGAD00001000060
Acral melanoma study whole genomes
Complete Genomics
3
EGAD00001000061
Acral melanoma study whole exomes
Illumina Genome Analyzer IIx
3
EGAD00001000062
ADCC Rearrangement Screen
Illumina Genome Analyzer II
Illumina HiSeq 2000
14
EGAD00001000063
Triple Negative Breast Cancer sequencing
Illumina Genome Analyzer II
6
EGAD00001000064
Cell Line Sub Clone Rearrangement Screen
Illumina Genome Analyzer II
6
EGAD00001000065
Mixed Leukemia Rearrangement Screen
Illumina Genome Analyzer II
5
EGAD00001000066
Breast Cancer Follow Up Series
Illumina Genome Analyzer II
288
EGAD00001000067
Cancer Single Cell Sequencing
Illumina HiSeq 2000
16
EGAD00001000068
Multifocal Breast Project
Illumina Genome Analyzer II
Illumina HiSeq 2000
22
EGAD00001000069
Lung Rearrangement Study
Illumina HiSeq 2000
48
EGAD00001000070
TMD_AMLK Exome Study
Illumina HiSeq 2000
50
EGAD00001000071
Kaposi sarcoma exome
Illumina HiSeq 2000
20
EGAD00001000072
Fanconi Anemia transformation to AML
Illumina HiSeq 2000
6
EGAD00001000073
MDSMPN Rearrangement Screen
Illumina HiSeq 2000
11
EGAD00001000074
Integrative Oncogenomics of Multiple Myeloma
Illumina Genome Analyzer II
Illumina HiSeq 2000
174
EGAD00001000075
Gastric and Esophageal tumour rearrangement screen
Illumina HiSeq 2000
32
EGAD00001000076
CRLF2 sequencing project
Illumina HiSeq 2000
13
EGAD00001000077
CRLF2 sequencing project Exomes
Illumina HiSeq 2000
26
EGAD00001000078
ALK inhibitors in the context of ALK-dependent cancer cell lines
Illumina HiSeq 2000
16
EGAD00001000079
PREDICT
Illumina HiSeq 2000
186
EGAD00001000080
Genomics of Colorectal Cancer Metastases - Massively Parallel Sequencing of Matched Primary and Metastatic tumours to Identify a Metastatic Signature of Somatic Mutations (MOSAIC)
Illumina HiSeq 2000
351
EGAD00001000081
Splenic Marginal Zone Lymphoma with villous lymphocytes exome sequencing
Illumina HiSeq 2000
1
EGAD00001000082
20 Matched Pair Breast Cancer Genomes
Illumina Genome Analyzer II
Illumina HiSeq 2000
42
EGAD00001000083
Recurrent Somatic Mutations in CLL
Illumina Genome Analyzer II
Illumina Genome Analyzer IIx
61
EGAD00001000084
Matched Ovarian Cancer Sequencing
Illumina Genome Analyzer II
23
EGAD00001000085
Somatic Histone H3 mutations
Illumina HiSeq 2000
14
EGAD00001000086
Analysis of genomic integrity of disease-corrected human induced pluripotent stem cells by exome sequencing
Illumina HiSeq 2000
16
EGAD00001000087
exome sequence data for 25 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000047) of raw BAMs mapped to GRCh37_53.
Illumina HiSeq 2000
25
EGAD00001000088
ER-, HER2-, PR- breast Cancer genome sequencing
Illumina Genome Analyzer II
6
EGAD00001000089
Acute Lymphoblastic Leukemia Exome sequencing
Illumina Genome Analyzer II
20
EGAD00001000090
Glioma cell lines rearrangement screen
Illumina Genome Analyzer II
3
EGAD00001000091
Non Tumour Renal Cell Line Sequencing
Illumina Genome Analyzer II
1
EGAD00001000092
Cancer Exome Resequencing
Illumina Genome Analyzer II
58
EGAD00001000093
Breast Cancer Exome Resequencing
Illumina Genome Analyzer II
21
EGAD00001000094
Cancer Genome Libraries Tests
Illumina Genome Analyzer II
16
EGAD00001000095
Acute Myeloid Leukemia Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
9
EGAD00001000096
Pancreatic adenocarcinoma QCMG 20120201
AB SOLiD 4 System
166
EGAD00001000097
Matched breast cancer fusion gene study
Illumina Genome Analyzer II
Illumina HiSeq 2000
46
EGAD00001000098
FRCC Exome sequencing
Illumina Genome Analyzer II
16
EGAD00001000099
Meningioma Exome
Illumina Genome Analyzer II
26
EGAD00001000100
Renal Matched Pair Cell Line Exome Sequencing
Illumina Genome Analyzer II
10
EGAD00001000101
ADCC Exome Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
125
EGAD00001000102
Myeloproliferative Disorder Sequencing
Illumina Genome Analyzer II
6
EGAD00001000103
Myeloproliferative Disorder Sequencing
Illumina Genome Analyzer II
4
EGAD00001000104
Acute Lymphoblastic Leukemia Exome sequencing 2
Illumina Genome Analyzer II
97
EGAD00001000105
MuTHER adipose tissue small RNA expression
Illumina Genome Analyzer II
130
EGAD00001000106
Primary Myelofibrosis Myeloproliferative Disease exome sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
67
EGAD00001000107
SCAT osteosarcoma sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
114
EGAD00001000108
Paroxysmal neurological disorders
Illumina Genome Analyzer II
Illumina HiSeq 2000
327
EGAD00001000109
Unraveling the genetic basis of a collagen migration defect in patients with a combined platelet dysfunction and reduced bone density
Illumina HiSeq 2000
29
EGAD00001000110
Breast Cancer Exome Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
179
EGAD00001000111
CML Discovery Project
Illumina Genome Analyzer II
6
EGAD00001000112
Identifying Novel Fusion Genes in Myeloma
Illumina Genome Analyzer II
6
EGAD00001000113
Mutational landscapes of primary triple negative breast cancers - Exomes
Illumina Genome Analyzer IIx
108
EGAD00001000115
Mutational landscapes of primary triple negative breast cancers - WGS
ABI_SOLID
32
EGAD00001000116
Acute Lymphoblastic Leukemia Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
61
EGAD00001000117
Myelodysplastic Syndrome Exome Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
152
EGAD00001000118
Osteosarcoma Exome Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
102
EGAD00001000119
Chordoma Exome Sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
50
EGAD00001000121
Breast Cancer Whole Genome Sequencing
Illumina HiSeq 2000
6
EGAD00001000122
DATA_SET_ICGC_PedBrainTumor_Medulloblastoma
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
206
EGAD00001000123
Polycythemia Vera Myeloproliferative Disease exome sequencing
Illumina Genome Analyzer II
Illumina HiSeq 2000
119
EGAD00001000124
Sequencing Acute Myeloid Leukaemia
Illumina HiSeq 2000
4
EGAD00001000125
Chondrosarcoma Exome
Illumina HiSeq 2000
104
EGAD00001000126
HER2 positive Breast Cancer
Illumina HiSeq 2000
101
EGAD00001000127
Burden of Disease in Sarcoma
Illumina HiSeq 2000
220
EGAD00001000128
Familial Thrombocytosis germline exome sequencing
Illumina HiSeq 2000
4
EGAD00001000129
Essential Thrombocythemia Myeloproliferative Disease exome sequencing
Illumina HiSeq 2000
189
EGAD00001000130
Breast Cancer Matched Pair Cell Line Whole Genomes
Illumina HiSeq 2000
22
EGAD00001000131
Genetic landscape of hepatocellular carcinoma
Illumina HiSeq 2000
48
EGAD00001000132
Mutational landscapes of primary triple negative breast cancers - RNA seq
Illumina Genome Analyzer IIx
80
EGAD00001000133
The landscape of cancer genes and mutational processes in breast cancer
Illumina Genome Analyzer II
Illumina HiSeq 2000
199
EGAD00001000134
Sequence reads for pediatric GBM samples for manuscript: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma
Illumina HiSeq 2000
54
EGAD00001000135
Neuroblastoma whole genome sequencing
Illumina HiSeq 2000
80
EGAD00001000136
CML blast phase rearrangement screen
Illumina HiSeq 2000
6
EGAD00001000138
The expression data for this study can be found here: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1088/and its SNP6 data can be found here:http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1087/
Illumina Genome Analyzer II
Illumina HiSeq 2000
58
EGAD00001000139
Tumor sample of a serious ovarian carcinoma
Complete Genomics
1
EGAD00001000140
Blood sample of serious ovarian carcinoma patient
Complete Genomics
1
EGAD00001000141
Triple Negative Breast Cancer Whole Genomes
Illumina Genome Analyzer II
Illumina HiSeq 2000
243
EGAD00001000142
Renal Follow Up Series
Illumina HiSeq 2000
637
EGAD00001000143
Xenograft Seqeuncing
Illumina HiSeq 2000
16
EGAD00001000144
Lung Cancer Whole Genomes
Illumina HiSeq 2000
18
EGAD00001000145
Matched Pair Cancer Cell line Whole Genomes
Illumina HiSeq 2000
58
EGAD00001000147
Osteosarcoma Whole Genome
Illumina HiSeq 2000
108
EGAD00001000149
A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome
Illumina HiSeq 2000
2
EGAD00001000150
Targeted re-sequencing of 97 genes in T-ALL
454 GS FLX Titanium
33
EGAD00001000151
UK10K OBESITY REL-2011-07-14
Illumina HiSeq 2000
88
EGAD00001000152
UK10K_RARE_THYROID REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
27
EGAD00001000153
UK10K_RARE_SIR REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
38
EGAD00001000154
Single-cell genome sequencing reveals DNA-mutation per cell cycle
Illumina Genome Analyzer II
Illumina HiSeq 2000
12
EGAD00001000158
Subgroup-specific structural variation across 1,000 medulloblastoma genomes
23
EGAD00001000159
DATA FILES FOR SJOS
Illumina HiSeq 2000
37
EGAD00001000160
DATA FILES FOR SJACT
Illumina HiSeq 2000
16
EGAD00001000161
DATA FILES FOR SJLGG
Illumina HiSeq 2000
33
EGAD00001000162
DATA FILES FOR SJEPD
Illumina HiSeq 2000
44
EGAD00001000163
DATA FILES FOR SJPHALL
Illumina HiSeq 2000
18
EGAD00001000164
Whole Genome Sequencing accompanying Genetic landscape of pediatric Rhabdomyosarcoma.
Illumina HiSeq 2000
29
EGAD00001000165
DATA FILES FOR SJINF
Illumina HiSeq 2000
46
EGAD00001000167
UK10K_RARE_HYPERCHOL REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
48
EGAD00001000168
UK10K_RARE_CILIOPATHIES REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
50
EGAD00001000170
UK10K_NEURO_MUIR REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
167
EGAD00001000171
UK10K_RARE_FIND REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
44
EGAD00001000173
UK10K_NEURO_ASD_FI REL-2012-01-13
Illumina HiSeq 2000
85
EGAD00001000174
DATA_SET_Coverage_bias_sensitivity_of_variant_calling_for_4_WG_seq_tech
AB SOLiD 4 System
Complete Genomics
Illumina HiSeq 2000
unspecified
4
EGAD00001000175
Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma
Illumina Genome Analyzer II
48
EGAD00001000176
DATA_SET_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
8
EGAD00001000177
Whole Genome Methylation in CLL
Illumina Genome Analyzer IIx
6
EGAD00001000178
UK10K_RARE_CHD REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
46
EGAD00001000179
UK10K_RARE_COLOBOMA REL-2012-01-13
Illumina Genome Analyzer II
Illumina HiSeq 2000
75
EGAD00001000180
UK10K_RARE_NEUROMUSCULAR REL-2012-01-13
Illumina HiSeq 2000
47
EGAD00001000181
UK10K_OBESITY_SCOOP REL-2012-01-13
Illumina HiSeq 2000
212
EGAD00001000182
UK10K_NEURO_UKSCZ REL-2012-01-13
Illumina HiSeq 2000
95
EGAD00001000183
UK10K_NEURO_FSZNK REL-2012-01-13
Illumina HiSeq 2000
273
EGAD00001000184
UK10K_NEURO_FSZ_REL_2012_01_13
Illumina HiSeq 2000
120
EGAD00001000185
UK10K_RARE_COLOBOMA REL-2012-02-22
Illumina Genome Analyzer II
Illumina HiSeq 2000
98
EGAD00001000186
UK10K_RARE_HYPERCHOL REL-2012-02-22
Illumina Genome Analyzer II
Illumina HiSeq 2000
71
EGAD00001000187
UK10K_RARE_THYROID REL-2012-02-22
Illumina Genome Analyzer II
Illumina HiSeq 2000
65
EGAD00001000188
UK10K_RARE_SIR REL-2012-02-22
Illumina Genome Analyzer II
Illumina HiSeq 2000
63
EGAD00001000189
UK10K_RARE_NEUROMUSCULAR REL-2012-02-22
Illumina HiSeq 2000
86
EGAD00001000190
UK10K_RARE_FIND REL-2012-02-22
Illumina Genome Analyzer II
Illumina HiSeq 2000
90
EGAD00001000191
UK10K_RARE_CILIOPATHIES REL-2012-02-22
Illumina Genome Analyzer II
Illumina HiSeq 2000
128
EGAD00001000192
UK10K_RARE_CHD REL-2012-02-22
Illumina Genome Analyzer II
Illumina HiSeq 2000
46
EGAD00001000193
UK10K_OBESITY_SCOOP REL-2012-02-22
Illumina HiSeq 2000
573
EGAD00001000194
UK10K_COHORT_TWINS REL-2011-12-01
Illumina Genome Analyzer II
Illumina HiSeq 2000
1713
EGAD00001000195
For information about this sample set, please contact the sample custodian Nic Timpson: N.J.Timpson@bristol.ac.uk
Illumina HiSeq 2000
740
EGAD00001000196
Neuroblastoma samples
Complete Genomics
203
EGAD00001000197
Progressive Hearing Loss
Illumina Genome Analyzer II
8
EGAD00001000198
Gene Discovery in Age-Related Hearing Loss
Illumina Genome Analyzer II
Illumina HiSeq 2000
20
EGAD00001000199
ORCADES_WGA
Illumina HiSeq 2000
400
EGAD00001000200
Dilgom Exome
Illumina HiSeq 2000
130
EGAD00001000201
MDACC-endo
AB SOLiD System 3.0
28
EGAD00001000202
Neuroblastoma samples (Analyses_vcf files)
204
EGAD00001000203
Otosclerosis gene discovery
Illumina HiSeq 2000
10
EGAD00001000204
Hearing loss in adults from South Carolina
Illumina HiSeq 2000
10
EGAD00001000205
BRAF and MEK resistant cell line clones
Illumina HiSeq 2000
3
EGAD00001000206
UK10K_RARE_COLOBOMA REL-2012-07-05
Illumina Genome Analyzer II
Illumina HiSeq 2000
123
EGAD00001000207
UK10K_RARE_HYPERCHOL REL-2012-07-05
Illumina Genome Analyzer II
Illumina HiSeq 2000
88
EGAD00001000208
UK10K_RARE_THYROID REL-2012-07-05
Illumina Genome Analyzer II
Illumina HiSeq 2000
65
EGAD00001000209
UK10K_RARE_FIND REL-2012-07-05
Illumina Genome Analyzer II
Illumina HiSeq 2000
121
EGAD00001000210
UK10K_RARE_CHD REL-2012-07-05
Illumina Genome Analyzer II
Illumina HiSeq 2000
124
EGAD00001000212
Functional characterisation of CpG islands in human tissues
Illumina Genome Analyzer II
26
EGAD00001000213
Screening for abnormal CGI methylation in primary colorectal tumours
Illumina Genome Analyzer II
21
EGAD00001000214
Whole genome sequencing of colon samples
Illumina HiSeq 2000
11
EGAD00001000215
RNA sequencing of colon tumor/normal sample pairs
Illumina HiSeq 2000
139
EGAD00001000216
Exome capture sequencing of colon tumor/normal pairs
Illumina HiSeq 2000
144
EGAD00001000217
UK10K_RARE_CILIOPATHIES REL-2012-07-05
Illumina Genome Analyzer II
Illumina HiSeq 2000
150
EGAD00001000218
UK10K_RARE_SIR REL-2012-07-05
Illumina Genome Analyzer II
Illumina HiSeq 2000
81
EGAD00001000219
UK10K_RARE_NEUROMUSCULAR REL-2012-07-05
Illumina HiSeq 2000
117
EGAD00001000220
Deep sequencing of CTCs
454 GS FLX Titanium
Illumina MiSeq
3
EGAD00001000221
Whole genome sequencing of SCLC tumor/normal samples
Illumina HiSeq 2000
4
EGAD00001000222
Exome capture sequencing of SCLC tumor/normal pairs and cell lines
Illumina HiSeq 2000
103
EGAD00001000223
RNA sequencing of SCLC tumor/normal sample pairs and cell lines
Illumina HiSeq 2000
79
EGAD00001000224
Enrichment of CRC
454 GS FLX Titanium
2
EGAD00001000225
Deep sequencing of KRAS
454 GS FLX Titanium
8
EGAD00001000226
Chordoma is a rare malignant bone tumor that expresses the transcription factor T. We conducted an association study of 40 patients with chordoma and 358 ancestry-matched, unaffected individuals with replication in an independent cohort. Whole-exome and Sanger sequencing of T exons reveals a strong risk association ( allelic odds ratio (OR) = 4.9, P = 3.3x10-11, CI= 2.9-8.1) with the common (minor allelic frequency >5%) non-synonymous SNP rs2305089 in chordoma, which is exceptional in cancer genetics.
Illumina Genome Analyzer II
Illumina HiSeq 2000
18
EGAD00001000227
EGAD00001000227_UK10K_NEURO_ABERDEEN_REL_2012_07_05
Illumina HiSeq 2000
347
EGAD00001000228
EGAD00001000228_UK10K_NEURO_ASD_BIONED_REL_2012_07_05
Illumina HiSeq 2000
59
EGAD00001000229
EGAD00001000229_UK10K_NEURO_ASD_FI_REL_2012_07_05
Illumina HiSeq 2000
85
EGAD00001000230
EGAD00001000230_UK10K_NEURO_ASD_GALLAGHER_REL_2012_07_05
Illumina HiSeq 2000
72
EGAD00001000231
EGAD00001000231_UK10K_NEURO_ASD_SKUSE_REL_2012_07_05
Illumina HiSeq 2000
320
EGAD00001000232
EGAD00001000232_UK10K_NEURO_ASD_TAMPERE_REL_2012_07_05
Illumina HiSeq 2000
54
EGAD00001000233
EGAD00001000233_UK10K_NEURO_EDINBURGH_REL_2012_07_05
Illumina HiSeq 2000
219
EGAD00001000234
EGAD00001000234_UK10K_NEURO_FSZNK_REL_2012_07_05
Illumina HiSeq 2000
281
EGAD00001000235
EGAD00001000235_UK10K_NEURO_IOP_COLLIER_REL_2012_07_05
Illumina HiSeq 2000
170
EGAD00001000236
EGAD00001000236_UK10K_NEURO_MUIR_REL_2012_07_05
Illumina Genome Analyzer II
Illumina HiSeq 2000
167
EGAD00001000237
EGAD00001000237_UK10K_NEURO_GURLING_REL_2012_07_05
Illumina HiSeq 2000
43
EGAD00001000239
EGAD00001000239_UK10K_NEURO_IMGSAC_REL_2012_07_05
Illumina HiSeq 2000
114
EGAD00001000240
UK10K_NEURO_FSZ_REL_2012_07_05
Illumina HiSeq 2000
120
EGAD00001000241
EGAD00001000241_UK10K_OBESITY_SCOOP_REL_2012_07_05
Illumina HiSeq 2000
674
EGAD00001000242
EGAD00001000242_UK10K_NEURO_ASD_MGAS_REL_2012_07_05
Illumina HiSeq 2000
60
EGAD00001000243
Melanoma-TIL Study Exomes
Illumina HiSeq 2000
43
EGAD00001000245
Pulldown cytosine deaminases
Illumina HiSeq 2000
20
EGAD00001000246
Integrative Oncogenomics of multiple myeloma
Illumina HiSeq 2000
106
EGAD00001000247
Integrative Oncogenomics of multiple myeloma
Illumina HiSeq 2000
51
EGAD00001000248
RNAseq Pulldown
Illumina HiSeq 2000
6
EGAD00001000249
This is the bam file generated after alignment using BWA program for the SAIF genome
Illumina HiSeq 2000
1
EGAD00001000251
De novo mutations in schizophrenia
Illumina HiSeq 2000
611
EGAD00001000252
Evaluation of PCR library method on whole genome samples
Illumina HiSeq 2000
12
EGAD00001000253
AML targeted resequencing study
Illumina HiSeq 2000
-
EGAD00001000254
This dataset contain the raw files generated for SAIF genome project
Illumina HiSeq 2000
1
EGAD00001000255
Testing the feasibility of genome scale sequencing in routinely collected FFPE cancer specimens versus matched fresh frozen samples
Illumina HiSeq 2000
32
EGAD00001000256
UK10K_NEURO_UKSCZ REL-2012-07-05
Illumina HiSeq 2000
595
EGAD00001000258
Deep RNA sequencing in CLL
Illumina Genome Analyzer II
107
EGAD00001000259
DATA FILES FOR SJAMLM7
Illumina HiSeq 2000
8
EGAD00001000260
Hypodiploid acute lymphoblastic leukemia whole genome sequencing
Illumina HiSeq 2000
40
EGAD00001000261
Retinoblastoma whole genome sequencing
Illumina HiSeq 2000
8
EGAD00001000262
OICR PANCREATIC CANCER DATASET
4
EGAD00001000263
A small subsample of EGAD00001000689. Please do not use.
Illumina HiSeq 2000
18
EGAD00001000264
Resistance towards chemotherapy is one of the main causes of treatment failure and deathamong breast cancer patients.The main objective of this project is toidentify genetic mechanisms causing some breast cancer patients not torespond to a particluar type of chemotherapy (epirubicin) while otherpatients respond very well to the same treatment. In the project wewill perform genome / exome sequencing of a selection of breast cancerpatients (n=30). These patients are drawn from a cohort where allpatients have recieved treatment with epirubicin monotherapy before surgical removal of alocally advanced breast tumour, and where all patients have beensubjected to objective evaluation of the response to thetherapy. Subsequent to sequencing, we will analyse the data andcompare with the clinical data for each patient (object response totherapy). The main aim being to identify mutations that are associatedwith resistance to epirubicin. Identification of mutations with strongpredictive value, may have a direct impact on cancer treatment sinceit opens the possibility for genetic testing of a tumour, and desicionon which drug is likely to work best, prior to treatment start.
Illumina HiSeq 2000
29
EGAD00001000265
This Study uses a focused bespoke bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.
Illumina HiSeq 2000
-
EGAD00001000266
This Study uses a focused bespoke bait pull down library method to target findings of Osteosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.
Illumina HiSeq 2000
110
EGAD00001000267
This Study uses a focused bespoke bait pull down library method to target findings of Chordoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.
Illumina HiSeq 2000
46
EGAD00001000268
DATA FILES FOR SJCBF
Illumina HiSeq 2000
34
EGAD00001000269
OLD DATA FILES FOR SJMB - Superseded by EGAD00001001864
Illumina HiSeq 2000
68
EGAD00001000270
DATA_SET_EOP-PCA-LargeAndSmallTumors1
Illumina HiSeq 2000
18
EGAD00001000271
Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood
Illumina HiSeq 2000
10
EGAD00001000272
Genomic Alterations in Gingivo-buccal Cancer: ICGC-India Project_YR01
454 GS FLX Titanium
Illumina HiSeq 2000
200
EGAD00001000273
This Study uses a focused bespoke bait pull down library method to target findings of Meningioma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.
Illumina HiSeq 2000
147
EGAD00001000274
DATA_SET_TRANSCIPTOME_Comparing_sequencing_four_proto-typical_Burkitt_lymphomas_BL_IG-MYC_translocation
Illumina HiSeq 2000
4
EGAD00001000275
Data set for Whole-genome-Sequencing of adult medulloblastoma
Illumina HiSeq 2000
10
EGAD00001000276
OICR PANCREATIC CANCER DATASET 2
10
EGAD00001000277
High Quality Variant Call files, generated by bioscope, converted to vcf format. Complete dataset for all 300 samples.
202
EGAD00001000278
ICGC MMML-seq Data Freeze November 2012 whole genome sequencing
Illumina HiSeq 2000
12
EGAD00001000279
ICGC MMML-seq Data Freeze November 2012 whole exome sequencing
Illumina Genome Analyzer IIx
4
EGAD00001000280
This experiment is to validate putative somatic substitutions and indels identified in an exome screen of ~50 osteosarcoma tumour/normal pairs. It is the first stage in our ICGC commitment to study osteosarcoma. The validation process is an important component of our analysis to clarify the data prior to looking for evidence of new cancer genes, or subverted pathways important in the development of cancer. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
112
EGAD00001000281
ICGC MMML-seq Data Freeze November 2012 transcriptome sequencing
Illumina HiSeq 2000
6
EGAD00001000282
Neuroblastomas are tumors of peripheral sympathetic neurons and are the most common solid tumor in children. To determine the genetic basis for neuroblastoma we performed whole-genome sequencing (6 cases), exome sequencing (16 cases), genome-wide rearrangement analyses (32 cases), and targeted analyses of specific genomic loci (40 cases) using massively parallel sequencing. On average each tumor had 19 somatic alterations in coding genes (range, 3-70). Among genes not previously known to be involved in neuroblastoma, chromosomal deletions and sequence alterations of chromatin remodeling genes, ARID1A and ARID1B, were identified in 8 of 71 tumors (11%) and were associated with early treatment failure and decreased survival. Using tumor-specific structural alterations, we developed an approach to identify rearranged DNA fragments in sera, providing personalized biomarkers for minimal residual disease detection and monitoring. These results highlight dysregulation of chromatin remodeling in pediatric tumorigenesis and provide new approaches for the management of neuroblastoma patients.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
114
EGAD00001000283
Agilent whole exome hybridisation capture was performed on genomic DNA derived from MDS and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to discover the prevalence of our findings using bespoke pulldown methods and sequencing the products from a larger set of patient DNA.
Illumina HiSeq 2000
764
EGAD00001000284
Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing
Illumina Genome Analyzer IIx
1
EGAD00001000285
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina Genome Analyzer II
Illumina HiSeq 2000
55
EGAD00001000286
Whole-exome study of congenital macrothrombocytopenia
Illumina HiSeq 2000
21
EGAD00001000287
Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.
Illumina Genome Analyzer II
54
EGAD00001000288
Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer accounting for 10-15% of cases. ILC differs from invasive ductal carcinoma (IDC)with respect to epidemiology, histology, and clinical presentation. Moreover, ILC is lesssensitive to chemotherapy, more frequently bilateral, and more prone to form gastrointestinal, peritoneal, and ovarian metastases than IDCs. In contrast to IDC, the prognostic value ofhistological grade (HG) in ILC is controversial. One of the three major components of histological grading (tubule formation) is missing in ILC which hinders the process of gradingin this histological subtype and results in the classification of approximately two thirds of ILC as HG 2.Over the last decade, a number of gene expression signatures have shed light onto breast cancer classification, allowing breast cancer care to become more personalized. Withrespect to the management of estrogen receptor (ER)-positive breast cancer, several gene expression signatures provide prognostic and/or predictive information beyond what is possible with current classical clinico-pathological parameters alone. Nevertheless, most studies using gene expression signature have not considered different histologic subtypesseparately. Recently, a comprehensive research program has elucidated some of the biological underpinnings of invasive lobular carcinoma. Genetic material extracted from 200 ILC tumor samples were studied using gene expression profiling and identified ILCmolecular subtypes. These proliferation-driven gene signatures of ILC appear to have prognostic significance. In particular, the Genomic Grade (GG) gene signature improved upon HG in ILC and added prognostic value to classic clinico-pathologic factors. In addition this study demonstrated that most ILC are molecularly characterized as luminal-A (~75%)followed by luminal-B (~20%) and HER2-positve tumors (~5%). Moreover, we investigated the prognostic value of known gene signatures/ gene modules in the same cohort of ILC. As a second step within the scope of this project, we aim to investigate the interactionsbetween somatic ILC tumor mutations to observed transcriptome findings. To this end, we aim to perform somatic mutation analysis for the ILC tumors for which Affymetrix gene expression profiling is available. To this end, we will use a gene screen assay, which specifically interrogates the mutational status of a few hundreds of cancer genes. We believe that this pioneering effort will be fundamental for a tailored treatment of ILC withimprovement in patients' outcome.
Illumina HiSeq 2000
1130
EGAD00001000289
Agilent whole exome hybridisation capture was performed on genomic DNA derived from cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.
Illumina HiSeq 2000
12
EGAD00001000290
Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing
Illumina Genome Analyzer IIx
1
EGAD00001000291
Exome sequencing identifies mutation of the ribosome in T-cell acute lymphoblastic leukemia
Illumina HiSeq 2000
128
EGAD00001000292
Whole genome sequencing analysis was performed on 6 patients within matched germline, follicular lymphoma and transformed follicular lymphoma.
Illumina HiSeq 2000
20
EGAD00001000293
Sequencing data for Australian Ovarian Cancer study submitted 20121116
AB SOLiD 4 System
72
EGAD00001000294
UK10K_RARE_CHD REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
124
EGAD00001000295
UK10K_RARE_HYPERCHOL REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
120
EGAD00001000296
UK10K_RARE_CILIOPATHIES REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
108
EGAD00001000297
UK10K_RARE_FIND REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
124
EGAD00001000298
UK10K_RARE_NEUROMUSCULAR REL-2012-11-27
Illumina HiSeq 2000
130
EGAD00001000299
Whole exome sequencing of samples selected from the Finrisk sample collection. The samples sequenced in this study have all been collected in Kuusamo, Finland.
Illumina HiSeq 2000
24
EGAD00001000300
UK10K_OBESITY_GS_REL_2012_07_05
Illumina HiSeq 2000
430
EGAD00001000301
A couple of previously characterized and sequenced libraries will be repeated using a couple of differing size selection criteria and skim sequenced using an Illumina HiSeq. The resulting sequence will be analyzed to determine the optimal DNA library size for our specific downstream analysis.
Illumina HiSeq 2000
1
EGAD00001000302
This experiment is looking at the mutational signatures generated by engineered HRAS mutations by using whole genome sequence generated on massively parallel next generation sequencers.
Illumina HiSeq 2000
6
EGAD00001000303
ICGC prostate cancer whole genome mate-pair sequencing
Illumina Genome Analyzer IIx
22
EGAD00001000304
ICGC prostate cancer miRNA sequencing
Illumina HiSeq 2000
8
EGAD00001000305
ICGC prostate cancer RNA sequencing
Illumina HiSeq 2000
12
EGAD00001000306
ICGC prostate cancer whole genome sequencing
Illumina HiSeq 2000
22
EGAD00001000307
UK10K_RARE_COLOBOMA REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
117
EGAD00001000308
Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing
1
EGAD00001000309
UK10K_OBESITY_GS REL-2012-11-27
Illumina HiSeq 2000
424
EGAD00001000310
UK10K_NEURO_ASD_BIONED REL-2012-11-27
Illumina HiSeq 2000
76
EGAD00001000311
UK10K_NEURO_ASD_FI REL-2012-11-27
Illumina HiSeq 2000
84
EGAD00001000312
UK10K_NEURO_ASD_MGAS REL-2012-11-27
Illumina HiSeq 2000
96
EGAD00001000313
UK10K_NEURO_ASD_SKUSE REL-2012-11-27
Illumina HiSeq 2000
305
EGAD00001000314
UK10K_NEURO_ASD_TAMPERE REL-2012-11-27
Illumina HiSeq 2000
48
EGAD00001000315
UK10K_NEURO_ABERDEEN REL-2012-11-27
Illumina HiSeq 2000
313
EGAD00001000316
UK10K_NEURO_ASD_GALLAGHER REL-2012-11-27
Illumina HiSeq 2000
75
EGAD00001000317
UK10K_NEURO_EDINBURGH REL-2012-11-27
Illumina HiSeq 2000
214
EGAD00001000318
UK10K_NEURO_FSZ REL-2012-11-27
Illumina HiSeq 2000
119
EGAD00001000319
UK10K_NEURO_GURLING REL-2012-11-27
Illumina HiSeq 2000
48
EGAD00001000320
UK10K_NEURO_IMGSAC REL-2012-11-27
Illumina HiSeq 2000
111
EGAD00001000321
UK10K_NEURO_IOP_COLLIER REL-2012-11-27
Illumina HiSeq 2000
158
EGAD00001000322
UK10K_NEURO_MUIR REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
166
EGAD00001000323
Sequencing data for Australian Pancreatic Cancer study submitted 20130102
AB SOLiD 4 System
Illumina HiSeq 2000
200
EGAD00001000324
We will sequence the RNA of lymphoblast samples, transformed with EBV, which have poikiloderma syndrome with mutations in c16orf57. The aim of the experiment is to characterise RNA structural effects in this disease.
Illumina HiSeq 2000
4
EGAD00001000325
In this study, mutations present in a series of human melanomas (stage IV disease) will be determined, using autologous blood cells to obtain a reference genome. From each of the samples that are analyzed, tumour-infiltrating T lymphocytes have also been isolated. This offers a unique opportunity to determine which (fraction of) mutations in human cancer leads to epitopes that are recognized by T cells. The resulting information is likely to be of value to understand how T cell activating drugs exert their action.
Illumina HiSeq 2000
22
EGAD00001000327
release_2: ICGC PedBrain: whole genome mate-pair sequencing
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
70
EGAD00001000328
ICGC PedBrain: RNA sequencing
Illumina HiSeq 2000
28
EGAD00001000329
UK10K_RARE_THYROID REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
113
EGAD00001000332
UK10K_NEURO_FSZNK REL-2012-11-27
Illumina HiSeq 2000
258
EGAD00001000333
Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing,s sarcoma tumours.
Illumina HiSeq 2000
58
EGAD00001000334
UK10K_RARE_SIR REL-2012-11-27
Illumina Genome Analyzer II
Illumina HiSeq 2000
111
EGAD00001000335
UK10K_NEURO_UKSCZ REL-2012-11-27
Illumina HiSeq 2000
527
EGAD00001000336
UK10K_OBESITY_SCOOP REL-2012-11-27
Illumina HiSeq 2000
784
EGAD00001000337
Illumina RNA-Seq will be performed on four Ewing's sarcoma cell lines and two control cell lines. RNA was extracted from all the lines using a basic Trizol extraction protocol.
Illumina HiSeq 2000
12
EGAD00001000338
We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
3
EGAD00001000339
Multiple myeloma is an incurable plasma cell malignancy whose molecular pathogenesis is incompletely understood. We used whole exome sequencing, copy number profiling and cytogenetic to analyses 84 samples from 67 patients with myeloma. In addition to known myeloma genes, we identify new candidate genes, including truncations of SP140, ROBO1 and FAT3 and clustered missense mutations in EGR1. We find oncogenic mutations in cancer genes not previously implicated in myeloma, including SF3B1, PI3KCA and PTEN. We define diverse processes contributing to the mutational repertoire, including kataegis and somatic hypermutation. Most cases have at least one cluster of subclonal variants, including subclonal driver mutations, implying on-going tumor evolution. Serial samples revealed diverse patterns of clonal evolution, including linear evolution, differential clonal response and branching evolution. Our findings reveal the myeloma genome to be heterogeneous across patients and, within individual patients, to exhibit diversity in clonal admixture and dynamics in response to therapy.
Illumina Genome Analyzer II
Illumina HiSeq 2000
154
EGAD00001000340
The objective of this study is to resequence of targeted intervals containing autosomal recessive variants causing neurological disorders in consanguineous pedigrees. Using homozygosity mapping, three intervals of very different sizes have previously been unambiguously mapped for three different neurological diseases: 2.4Mb, 8Mb and 14.3Mb in size, for Microlissencephaly, Severe Mental Retardation and Complicated hereditary spastic paraplegia respectively. This study is a pilot to assess how well custom targeted resequencing performs across a broad size range of intervals. The study design is to use a different custom capture probe set for each interval, pulldown from a single patient from each family, and sequence 1 lane using Illumina paired-reads for each sample. Candidate variants will be followed up in the families themselves, and in patients with similar phenotypes from outbred populations
Illumina Genome Analyzer II
3
EGAD00001000341
This pilot study aims to generate pilot data to inform future study designs in consanguineous families or inbred populations by resequencing the exome of six individuals from five families with neurodevelopmental diseases. For all of these families a single mapping interval containing the causal variant has previously been identified.
Illumina HiSeq 2000
6
EGAD00001000342
This project aims to find causal variants in 50 patients diagnosed with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD), of presumed recessive inheritance performing whole exome sequencing to ~50x mean depth.This is a collaboration with Prof A. Jackson, MRC Human Genetics Unit, Edinburgh
Illumina Genome Analyzer II
Illumina HiSeq 2000
66
EGAD00001000343
This project aims to identify highly penetrant coding variants increasing the risk of Congenital Heart Disease (CHD) performing whole exome sequencing on DNA samples from 23 affected individuals, selected from 10 families with presumed Autosomal Recessive Inheritance. This is a collaboration with Prof. Eamonn Maher and Dr. Chirag Patel from the Department of Medical and Molecular Genetics, University of Birmingham plans to sequence 23 indexed Agilent whole exome pulldown libraries on 75Bp PE HiSeq (Illumina)
Illumina HiSeq 2000
24
EGAD00001000344
Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome.
Illumina HiSeq 2000
90
EGAD00001000345
Exome sequencing of 12 DNA samples obtained from patients with structural brain malformations.
Illumina HiSeq 2000
9
EGAD00001000346
Exome sequencing of patients and their families with diverse rare neurological disorders. Some families have prior linkage data identifying a specific chromosomal interval or interest, other families do not have linkage data available. Many of these families come from special populations whose demography or preference for consanguineous marriages make them particularly tractable for genetic studies.
Illumina HiSeq 2000
30
EGAD00001000347
These samples include exome sequences of family members with dyslipidemias from Finnish origin.
Illumina HiSeq 2000
95
EGAD00001000348
This pilot study aims to generate pilot data to inform future study designs by resequencing the whole exomes of 10 unrelated individuals diagnosed with Bilateral Anophthalmia.
Illumina Genome Analyzer II
16
EGAD00001000349
These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy.
Illumina HiSeq 2000
33
EGAD00001000350
We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.
Illumina HiSeq 2000
17
EGAD00001000351
This pilot study aims to generate pilot data to inform future study designs by resequencing the whole exomes of 10 unrelated individuals diagnosed with Congenital Heart Disease (CHD).
Illumina Genome Analyzer II
16
EGAD00001000352
DATA FILES FOR SJLGG
Illumina HiSeq 2000
7
EGAD00001000353
DATA FILES FOR SJLGG
Illumina HiSeq 2000
45
EGAD00001000354
Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.
Illumina HiSeq 2000
81
EGAD00001000355
ICGC MMML-seq Data Freeze March 2013 whole genome sequencing
Illumina HiSeq 2000
46
EGAD00001000356
ICGC MMML-seq Data Freeze March 2013 transcriptome sequencing
Illumina HiSeq 2000
23
EGAD00001000357
PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced by MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
4
EGAD00001000358
Chondrosarcoma (CHS) is a heterogeneous collection of malignant bone tumours and is the second most common primary malignancy of bone after osteosarcoma. Recent work has identified frequent, recurrent mutations in IDH1/2 in nearly half of central CHS. However, there has been little systematic genomic analysis of this tumour type and thus the contribution of other genes is unclear. Here we report comprehensive genomic analyses of 49 cases of CHS. We identified hypermutability of the major cartilage collagen COL2A1 with insertions, deletions and rearrangements identified in 37% of cases. The patterns of mutation were consistent with selection for variants likely to impair normal collagen biosynthesis. In addition we identified mutations in IDH1/2 (59%), TP53 (20%), the RB1 pathway (27%) and hedgehog signaling (22%).
Illumina HiSeq 2000
17
EGAD00001000359
In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.
Illumina HiSeq 2000
2
EGAD00001000360
The genome-wide landscape of somatically acquired mutations in mesothelioma has not been deeply characterised to date, but advances in DNA sequencing technology now allow this to be addressed comprehensively. Harnessing massively parallel DNA sequencing platforms, we will identify somatically acquired point mutations in all coding regions of the genome from patients with mesothelioma. In addition, using paired-end sequencing, we will map copy number changes and genomic rearrangements from the same patients.
Illumina HiSeq 2000
232
EGAD00001000361
This is a small pilot data set to test the feasibility of cDNA exomes across 1200 cancer cell line panel. cDNA exomes or Fus-seq is further explained in this studies Abstract.
Illumina HiSeq 2000
3
EGAD00001000362
Human induced pluripotent stem (hiPS) cells hold great promise for regenerative medicine. Safety issues of use of hiPS cells however remain to be addressed. One of such issues is mutations derived from somatic donor cells and introduced during genome manipulation. We sequence whole genomes of hiPS cells and analyzed mutations. Our study brings hiPS cell technology one step closer to application to regenerative medicine.
Illumina HiSeq 2000
7
EGAD00001000363
Common variable immunodeficiency (CVID) is the most common form of primary immunodeficiency with an estimated incidence of 1:10,000. It has been apparent for many years that CVID has a genetic component, occurs frequently in families and can have both a recessive or dominant mode of inheritance. In recent years, 4 genes underlying CVID have been identified; however, mutations within in them are estimated to account for no more than 10% of all cases of CVID.
We have identified a multi-generational family with autosomal dominant CVID. Genome-wide linkage analysis has mapped the locus underlying CVID in this family to an approximately 9.2 Mb interval on chromosome 3q27.3-q29, between the markers D3S3570 and D3S1265. This locus is distinct from any of the previously mapped susceptibility loci suggesting a novel genetic variant is responsible for disease in this family. The aim of this study is to use exome sequencing of affected (n = 4) and unaffected (n = 4) individuals, in tandem with the available genetic mapping data, to identify the causal variant underlying CVID in this family.
Illumina HiSeq 2000
8
EGAD00001000364
We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9).
Illumina MiSeq
50
EGAD00001000365
In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit.
Illumina MiSeq
7
EGAD00001000366
WGBS data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years.
Illumina HiSeq 2000
52
EGAD00001000367
Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.
Illumina HiSeq 2000
5
EGAD00001000368
Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.
Illumina HiSeq 2000
3
EGAD00001000369
We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.
Illumina HiSeq 2000
3
EGAD00001000370
This dataset is compromised of 5 sequencing experiments from a single patient with sporadic and recurring parathyroid carcinoma. The samples include whole genome sequence of the primary tumor, the first recurrent tumor and peripheral blood. Whole transcriptome sequence of the first and second recurrent tumors are also included.
Illumina HiSeq 2000
5
EGAD00001000371
Sequencing data for PDAC cell lines generated by QCMG
Illumina HiSeq 2000
Illumina HiSeq 2500
54
EGAD00001000372
We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.
Illumina HiSeq 2000
24
EGAD00001000380
Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients.
Illumina Genome Analyzer II
Illumina HiSeq 2000
64
EGAD00001000381
Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients.
Illumina HiSeq 2000
3
EGAD00001000382
Whole Exome Sequencing of Permanent Neonatal Diabetes Patients
Illumina HiSeq 2000
25
EGAD00001000383
In collaboration with Dr Robert Semple we have identified a family harbouring an autosomal dominant variant, which leads to severe insulin resistance (SIR), short stature and facial dysmorphism. This family is unique within the SIR cohort in having normal lipid profiles, preserved adiponectin and normal INSR expression and phosphorylation. DNA is available for 7 affected and 7 unaffected family members across 3 generations. All 14 samples have been genotyped using microsatellites and the Affymetrix 6.0 SNP chip. Linkage analysis identified an 18.8Mb haplotype on chromosome 19 as a possible location of the causative variant. However, Exome sequencing of 3 affected and 1 unaffected family members has not identified the causative variant suggesting the possibility of an intronic or intergenic variant in this region or elsewhere in the genome. We propose to conduct whole genome sequencing of 5 members of the pedigree at a depth of 20X. The chosen samples are two sets of parents plus one member of an unaffected branch of the pedigree who shares the risk haplotype on chromosome 19. Sequencing of the two sets of parents will be used along with the genome-wide SNP data to impute 4 affected children giving an effect sample size of 6 affected individuals.
Illumina HiSeq 2000
7
EGAD00001000384
In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unlcear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types.
Illumina HiSeq 2000
35
EGAD00001000385
Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myeloproliferative Disease samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements.
Illumina HiSeq 2000
108
EGAD00001000386
Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myelodysplastic syndrome patient samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements.
Illumina HiSeq 2000
83
EGAD00001000387
This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.
Illumina HiSeq 2000
35
EGAD00001000388
Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.
Illumina HiSeq 2000
15
EGAD00001000389
Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours.
Illumina HiSeq 2000
20
EGAD00001000390
We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
101
EGAD00001000392
Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.
Illumina MiSeq
60
EGAD00001000393
Illumina HiSeq 2000
30
EGAD00001000394
DNA methylation has been shown to play a major role in determining cellular phenotype by regulating gene expression. Moreover, dysregulation of differentially methylated genes has been implicated in disease pathogenesis of various conditions including cancer development as well as autoimmune diseases such as systemic Lupus erythematosus and rheumatoid arthritis. Evidence is rapidly accumulating for a role of DNA methylation in regulating immune responses in health and disease. However, the exact mechanisms remain unknown. The overall aim of the project is to investigate the role of epigenetic mechanisms in regulating immunity and their impact on autoimmune disease pathogenesis.The aim of this pilot study is to perform whole genome methylation analysis in peripheral blood mononuclear cells (PBMCs) and cell subsets (CD4, CD8, CD14, CD19, CD16 and whole PBMCs) obtained from 6 healthy volunteers. Whole genome methylation analysis will be performed using two methodological approaches, the Infinium Methylation Bead Array K450 (Illumina) and MeDIP-seq. mRNA expression arrays will also be performed in order to correlate DNA methylation with gene expression as well as genotyping on the Illumina OmniExpress chip
Illumina Genome Analyzer II
6
EGAD00001000395
Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma
1
EGAD00001000396
We performed serial plasma-Seq analyses on a male who progressed from castration-sensitive to castration-resistant prostate cancer within 10 months following treatment with androgen-deprivation therapy.
Illumina MiSeq
2
EGAD00001000397
The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.
Illumina HiSeq 2000
47
EGAD00001000398
The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.
Illumina Genome Analyzer II
8
EGAD00001000399
In 2009 we identified a four-generation family with over 700 members and 41 affected with Crohn's disease (CD). At the time we sequenced the exome of 6 affected individuals but did not identify any coding variants which appear to explain the high prevalence of disease. Since then we have collected DNA from a large number of additional family members, genotyped linkage arrays on the entire family to refine genomic regions shared by identity by descent and genotyped affected and unaffected members at known CD risk loci identified by Genome Wide Association Studies (GWAS). These analyses have confirmed that a significant unexplained excess of disease remains after accounting for all known genetic factors, and that several regions of the genome are shared by a large fraction of affected individuals. We therefore perform whole genomes sequencing from 8 individuals which will allow us to impute the complete sequence of nearly all the members of the two largest and most severely affected branches of the family.
Illumina HiSeq 2000
8
EGAD00001000400
The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.
Illumina HiSeq 2000
12
EGAD00001000401
Population based sequencing of whole genomes of Crohn's disease patients.
Illumina HiSeq 2000
2926
EGAD00001000402
The study will analyse by exome sequencing 42 Greek patients with premature MI and no vessel disease to identify genetic factors underlying this condition.
Illumina HiSeq 2000
46
EGAD00001000403
The ENGAGE project is a FP7 funded EU project aiming to combine genetic and phenotype information from European population based cohorts. In this sub-project we aim to do whole exome sequencing of individuals selected from Health 2000 and FINRISK cohorts. Individuals have been selected based on their metabolic trait phenotypes
Illumina HiSeq 2000
394
EGAD00001000404
Acute myeloid leukaemia (AML) is an aggressive and molecularly diverse disease with a poor overall survival of 20-25%. With an annual incidence of 2.9 per 100,000, AML is currently the commonest myeloid malignancy in Europe, yet the two main therapeutic options for this disease, anthracyclines and purine analogues, have remained unchanged for over 20 years.
Currently patients are stratified at diagnosis according to a series
of clinicopathological parameters (e.g. age, white cell count and
presence/absence of previous clonal haematological disease) and
molecular markers (e.g. chromosomal translocations/deletions,
aneuploidy and mutations in genes such as FLT3 and NPM1). Patients
with adverse prognostic features, whose prognosis is particularly poor
(e.g. <15% long-term survival) are offered treatment with allogeneic bone marrow transplantation (allo-BMT) if a sibling or unrelated donor is available. This can significantly improve survival (e.g. up to 40% long-term survival in some contexts), albeit at the expense of significant toxicity and transplant-related mortality (TRM).
Allo-BMT is thought to work in part by allowing the delivery of large doses of chemotherapy followed by haemopoietic "rescue" with donor haemopoietic stem cells (haemopoietic failure would otherwise ensue). However, potentially the most potent effect of allo-BMT is the cytotoxic effect of donor lymphocytes against AML blasts, a phenomenon known as graft-vs-leukaemia (GVL) effect. Increasingly, transplants using reduced chemotherapy intensity (mini-allografts) are being used that partially circumvent the toxicity from chemotherapy and rely on GVL to effect cure.
Nevertheless, AML relapse after allo-BMT still occurs at a significant rate of up to 80% depending on the type of transplant. There is accumulating evidence that genetic events in residual leukaemic cells enable them to evade immunodetection and therefore survive the GVL effect and expand to cause relapse. The most striking example of this is the loss of HLA antigens after transplants in which donor and recipient are not fully HLA-matched. In these cases, the leukaemia "deletes" the genomic region containing the disparate HLA antigen which was preferentially targeted as "foreign" by the GVL effect. However, the genetic basis of immune evasion in the majority of transplants, which are fully HLA matched, is not known. One possibility is that loss of genes coding for antigens outside the HLA locus but which are also targets of GVL may operate, alternatively genetic events that affect processes downstream of immunological cytotoxicity may be responsible.
The identification of genetic events that mediate immune evasion would not only facilitate the understanding of this process but can help plan therapeutic interventions that improve the outcomes of allogeneic transplantation for AML and other disorders. We intend to study this by conducting exome sequencing on 6 cases of AMLs from patients that attend my clinic at Addenbrooke's hospital and have relapsed after allogeneic transplantation. Samples from AML diagnosis, remission/normal and AML relapse (total n=18) will be studied to identify somatic mutations in the primary AML and those acquired by the relapsed clone. The 18 samples will also be studied by array CGH to detect regions of genomic amplification or deletion.
Illumina HiSeq 2000
25
EGAD00001000405
In this project we will sequence the exomes of 250 patients with Parkinson's disease
Illumina HiSeq 2000
247
EGAD00001000406
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive haematological malignancy derived from precursors of plasmacytoid dendritic cells. Due to the rarity of BPDCNs our knowledge of their molecular pathogenesis was until recently confined to observations describing reccurent chromosomal deletions involving chromosomes 5q, 12p, 13q, 6q, 15q and 9. A recent publication went on to delineate the common deleted regions using aCGH and demonstrated that these centred around known tumour suppressor genes including CDKN2A/B (9p21.3), RB1 (12p13.2-14.3), CDKN1B (13q11-q12) and IKZF1 (7p12.2).
These mutations are found recurrently in several different cancers and in most cases are thought to be involved in tumour progression rather than initiation. However, the well-defined nature and cellular ontogeny of these neoplasms suggests strongly that they share one or a few characteristic mutations as has been demonstrated for other uncommon but well-defined neoplasms such as Hairy Cell Leukemia (BRAF) and ovarian Granulosa Cell tumours (FOXL2).
Illumina HiSeq 2000
14
EGAD00001000407
We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.
Illumina HiSeq 2000
327
EGAD00001000408
We aim to whole-exome sequence DNA samples from 75 individuals with severe forms of Inflammatory Bowel Disease and related autoimmune diseases to identify the rare, highly penetrant, variants that we believe underlie these phenotypes. Case samples will be obtained from both new and existing (UK IBD Genetics Consortium) collaborators to ensure only the most extreme cases are sequenced.
Illumina HiSeq 2000
4
EGAD00001000409
2000 ulcerative colitis cases drawn from the UKIBD Genetics
Consortium cohort and whole-genome sequenced at 2X depth. A case
control association study using control samples whole-genome sequenced
by UK10K will be undertaken to identify common, low-frequency and rare
variants associated with ulcerative colitis. Data will be combined
with similar data across 3000 Crohn's disease cases from the same
cohort to identify inflammatory bowel disease (IBD) loci and better
understand the genetic differences and similarities of the two common
forms of IBD.
Illumina HiSeq 2000
1992
EGAD00001000410
We will perform exome sequencing on selected cases of splenic marginal zone lymphoma (SMZL) and diffuse large B-cell lymphoma (DLBCL) in order to characterise their genetic makeup and identify biomarkers for prognosis and prediction of treatment response.
Illumina HiSeq 2000
78
EGAD00001000411
These samples include exome sequences of family members with dyslipidemias from northern Finnish origin.
Illumina HiSeq 2000
68
EGAD00001000412
We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.
Illumina HiSeq 2000
477
EGAD00001000413
UK10K_RARE_CHD REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
125
EGAD00001000414
UK10K_RARE_CILIOPATHIES REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
122
EGAD00001000415
UK10K_RARE_COLOBOMA REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
123
EGAD00001000416
UK10K_RARE_FIND REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
124
EGAD00001000417
UK10K_RARE_HYPERCHOL REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
125
EGAD00001000418
UK10K_RARE_NEUROMUSCULAR REL-2013-04-20
Illumina HiSeq 2000
140
EGAD00001000419
UK10K_RARE_SIR REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
121
EGAD00001000420
UK10K_RARE_THYROID REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
124
EGAD00001000421
The aim of this project is to identify rare variants in the 1q region associated with type 2 diabetes. To this end 651 case samples and 651 control samples from six populations have been pooled (pool sizes range from 27-33 individuals), and are being sequenced. The hybridization solution being used captures the exons and UTRs of genes in the 1q region.
Illumina HiSeq 2000
48
EGAD00001000422
We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples.
Illumina HiSeq 2000
86
EGAD00001000423
The aim is to find rare variants of intermediate penetrance in those at risk of Crohn's disease
Illumina Genome Analyzer II
10
EGAD00001000424
The aim of this project is to identify rare variants in the 1q region associated with type 2 diabetes. To this end 651 case samples and 651 control samples from six populations have been pooled (pool sizes range from 27-33 individuals), and are being sequenced. The hybridization solution being used captures the exons and UTRs of genes in the 1q region.
Illumina Genome Analyzer II
Illumina HiSeq 2000
23
EGAD00001000425
GENCORD2 RNA-seq BAM files using BWA
Illumina Genome Analyzer II
Illumina HiSeq 2000
568
EGAD00001000427
Illumina HiSeq 2000
30
EGAD00001000428
204 individuals were genotyped with the Illumina 2.5M Omni chip. Filtered genotypes were imputed into the 1000 genomes project European panel SNPs. Beagle R2 is indicated in VCF files for further filtering. See Materials and Methods in publication for details.
204
EGAD00001000429
UK10K_OBESITY_TWINSUK REL-2013-04-20
Illumina HiSeq 2000
68
EGAD00001000430
UK10K_NEURO_UKSCZ REL-2013-04-20
Illumina HiSeq 2000
554
EGAD00001000431
UK10K_OBESITY_GS REL-2013-04-20
Illumina HiSeq 2000
428
EGAD00001000432
UK10K_OBESITY_SCOOP REL-2013-04-20
Illumina HiSeq 2000
985
EGAD00001000433
UK10K_NEURO_ABERDEEN REL-2013-04-20
Illumina HiSeq 2000
392
EGAD00001000434
UK10K_NEURO_ASD_BIONED REL-2013-04-20
Illumina HiSeq 2000
77
EGAD00001000435
UK10K_NEURO_ASD_FI REL-2013-04-20
Illumina HiSeq 2000
84
EGAD00001000436
UK10K_NEURO_ASD_GALLAGHER REL-2013-04-20
Illumina HiSeq 2000
77
EGAD00001000437
UK10K_NEURO_ASD_TAMPERE REL-2013-04-20
Illumina HiSeq 2000
55
EGAD00001000438
UK10K_NEURO_EDINBURGH REL-2013-04-20
Illumina HiSeq 2000
234
EGAD00001000439
UK10K_NEURO_FSZNK REL-2013-04-20
Illumina HiSeq 2000
285
EGAD00001000440
UK10K_NEURO_GURLING REL-2013-04-20
Illumina HiSeq 2000
46
EGAD00001000441
UK10K_NEURO_IMGSAC REL-2013-04-20
Illumina HiSeq 2000
113
EGAD00001000442
UK10K_NEURO_IOP_COLLIER REL-2013-04-20
Illumina HiSeq 2000
172
EGAD00001000443
UK10K_NEURO_MUIR REL-2013-04-20
Illumina Genome Analyzer II
Illumina HiSeq 2000
175
EGAD00001000444
Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours.
Illumina HiSeq 2000
3
EGAD00001000445
We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose.
Illumina MiSeq
9
EGAD00001000446
Fastq files of 213 samples of hepatocellular carcinoma (NCCRI)
Illumina HiSeq 2000
213
EGAD00001000596
This project is to develop and validate a method to detect de novo mutations in a foetal genome through deep sequencing of cell-free DNA from the plasma of pregnant women.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
5
EGAD00001000597
Illumina HiSeq 2000
212
EGAD00001000598
The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.
Illumina HiSeq 2000
120
EGAD00001000599
We have collected material from a patient who had BrafV600E mutant melanoma that was
treated with PLX4032. We have germline DNA from the patient and DNA and RNA from
distinct lesions before and after treatment with PLX4032. We have transcriptome sequenced these samples to obtain a snap shot of the mechanisms of resistance that are operative.
Illumina HiSeq 2000
6
EGAD00001000601
Illumina HiSeq 2000
1
EGAD00001000602
Illumina HiSeq 2000
1
EGAD00001000603
We recently used the Agilent SureSelect platform to re-sequence a set of genes known to be
mutated in human AML. The results from 10 AML DNA samples were very satisfactory, but
the effort required was significant.
Thus, we decided to re-sequence the same genes using the Haloplax system for target
enrichment in 48 AML samples. We planned to do this using MiSeq and have data from a
pilot of 3 samples. The data is promising but coverage appears pathcy so far.
However, in order to get a better understanding of the data we will need deeper sequencing. We
will need two lanes of HiSeq to get the same degree coverage as Sureselect.
his data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
Illumina MiSeq
54
EGAD00001000604
In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The transcriptomes of these iPS cells will be compared.
Protocol: primary cultures of cells were reprogrammed to iPS cells. RNA was extracted using a standard column extraction kit.
Illumina HiSeq 2000
47
EGAD00001000605
CR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
Illumina MiSeq
10
EGAD00001000606
Background Massively parallel sequencing technology has transformed cancer genomics. It is now feasible, in a clinically relevant time-frame, for a clinically manageable cost, to screen DNA from patient tumours for mutations essentially genome-wide. The challenge for personalised medicine will be to increase the sample size to thousands or tens of thousands of well-characterised cases in order to attain sufficient statistical power to stratify patients accurately across the complexity and genomic heterogeneity expected for most of the common tumour types. Currently, whole genome sequencing on this scale is not feasible, and targeted sequencing of relevant portions of the genome will be required. Pilot data We have developed protocols for large-scale, multiplexed sequencing of 100-200 genes in thousands of samples. Essentially, using robotic technology, genomic DNA from the cancer specimen is processed into sequencing libraries with unique DNA barcodes, thereby allowing sequencing reads to be attributed to the sample they derive from. Currently, these sequencing libraries can be generated in a 96-well format using fully automated protocols, and we are exploring methods to expand this to a 384-well format. The sequencing libraries are pooled and hybridized to custom sets of RNA baits representing the genomic regions of interest. Sequencing of the pulled-down libraries is done in pools of 48-96 samples per lane of an Illumina Hi-Seq. This protocol is already implemented at the Sanger Institute. We have published proof that somatic mutations in novel cancer genes can be identified from exome-wide sequencing. In unpublished pilot data, we have established the feasibility of robotic library production, custom pull-down, and multiplexed sequencing of barcoded libraries for 100 known myeloid cancer genes across 760 myelodysplasia samples. Highlights of the data thus far analysed reveal that the coverage is remarkably even between samples; when 96 samples are run, average coverage per lane of sequencing is ~250, with 90-95% of targeted exons covered by >25 reads; known mutations can be discovered in the data set; and the protocol is amenable to whole genome amplified DNA. The bioinformatic algorithms for identification of substitutions and indels in pull-down data are well-established; we have pilot data proving that copy number changes, LOH and genomic rearrangements in specific regions of interest can also be identified by tiling of baits across the relevant loci. Proposal We propose to apply this methodology to 10000 samples from patients with AML enrolled in clinical trials over the last 10-20 years. Oncogenic point mutations and potentially genomic rearrangements will be identified, and linked to clinical outcome data, with a view to undertaking the following sorts of analyses: ? Identification of co-occurrence, mutual exclusivity and clusters of driver mutations. ? Correlation of prognosis with driver mutations and potentially gene-gene interactions ? Exploration of genomic markers of drug response Ultimately, we would like to be in a position to release the mutation data together with matched clinical outcome data to genuine medical researchers via a controlled access approach, possibly within the COSMIC framework (www.sanger.ac.uk/genetics/CGP/cosmic/). The vision here is to generate a portal whereby a clinician faced with an AML patient and his / her mutational profile can obtain a ?personalised? prediction of outcome, together with a fair assessment of the uncertainty of the estimate. With a sufficient sample size, there would also be the potential to develop decision support algorithms for therapeutic choices based on such data.
Illumina MiSeq
38
EGAD00001000607
PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
2
EGAD00001000608
PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
60
EGAD00001000609
Whole transcriptome sequencing of 28 untreated prostate cancers, 13 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.
Illumina HiSeq 2000
53
EGAD00001000610
Methylated DNA immunoprecipitation sequencing of 28 untreated prostate cancers, 11 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.
Illumina HiSeq 2000
51
EGAD00001000611
Small RNA sequencing of 28 untreated prostate cancers, 12 castration resistant prostate cancers, and 3 benign prostatic hyperplasias.
Illumina HiSeq 2000
43
EGAD00001000612
Low coverage whole genome sequencing of 27 untreated prostate cancers, 9 castration resistant prostate cancers, and 4 benign prostatic hyperplasias.
Illumina HiSeq 2000
40
EGAD00001000613
UK10K_NEURO_ASD_MGAS REL-2013-04-20
Illumina HiSeq 2000
97
EGAD00001000614
UK10K_NEURO_ASD_SKUSE REL-2013-04-20
Illumina HiSeq 2000
341
EGAD00001000615
UK10K_NEURO_FSZ REL-2013-04-20
Illumina HiSeq 2000
128
EGAD00001000616
Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing
Illumina HiSeq 2000
192
EGAD00001000617
Pilocytic Astrocytoma ICGC PedBrain RNA sequencing
Illumina HiSeq 2000
73
EGAD00001000618
1204 Sardinian males
1195
EGAD00001000619
Experiments using targeted pulldown methods will be sequenced to validate findings in the exomes of patients with Myeloproliferative Neoplasms (MPN).
Illumina HiSeq 2000
360
EGAD00001000620
A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.
Illumina HiSeq 2000
14
EGAD00001000621
We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331
Illumina MiSeq
18
EGAD00001000623
This VCF contains the full sequence data post QC. This consists of 41,911 individuals. All polymorphic sites are present in this VCF.
41911
EGAD00001000624
Multifocality or multicentricity in breast cancer may be defined as the presence of two or more tumor foci within a single quadrant of the breast or within different quadrants of the same breast, respectively. This original classification of the breast cancer as multicentric or multifocal was based on the assumption that cancers arising in the same quadrant were more likely to arise from the same ductal structures than those occurring in separate areas of the breast. The problem with these definitions is that the ?quadrants? of the breast are arbitrary external designations, as no internal boundaries do exist. This project will therefore focus both on synchronous multifocal and multicentric tumors. The incidence of multifocal and multicentric breast cancers was reported to be between 13 and 75% depending on the definition used, the extent of the pathologic sampling of the breast and whether in situ disease is considered evidence of multicentricity (1). Although this incidence is variable, those figures show that it is a frequent phenomenon. Multiple (multifocal/multicentric) breast carcinomas, especially when occurring in the same breast, represent a real challenge for both pathologists and clinicians in terms of identifying the cellular origin and the best therapeutic management of the cancer. Multifocality or multicentricity has been associated with a number of more aggressive features including an increased rate of regional lymph node metastases and adverse patient outcome when compared with unifocal tumors (2-3), and a possible increased risk of local recurrence following breast conserving surgery (4). For the moment, the literature is divided on whether there is a corresponding impact on survival outcomes. Today, the current convention to stage and to treat multifocal and multicentric tumors is the classical tumor-node-metastasis (TNM) staging guidelines with which tumor size is assessed by the largest tumor focus without taking other foci of disease into consideration. If some papers, as the recent one from Lynch and colleagues, support the current staging convention (3), others, however, as Boyages et al. suggested that aggregate size and not the size of the largest lesion should be considered in order to refine the prognostic assessment of those tumors (5). On the top of that, the question whether multifocal/multicentric carcinomas are due to the spread of a single carcinoma throughout the breast or is due to multiple carcinomas arising simultaneously has been a matter of debate. Some studies suggested that multifocal breast cancer may result from either intramammary spread from a single primary tumor or multiple synchronous primary tumors; whereas others suggest that multiple breast carcinomas always arise from the same clone (6-8). Recently, Pietri and colleagues analyzed the biological characterization of a series of 113 multifocal/multicentric breast cancers (8) which were diagnosed over a 5-year period. The expression of estrogen (ER) and progesterone (PgR) receptors, Ki-67 proliferative index, expression of HER2 and tumor grading were prospectively determined in each tumor focus, and mismatches among foci were recorded. Mismatches in ER status were present in 5 (4.4%) cases and PgR in 18 (15.9%) cases. Mismatches in tumor grading were present in 21 cases (18.6%), proliferative index (Ki-67) in 17 (15%) cases and HER2 status in 11 (9.7%) cases. Interestingly, this heterogeneity among foci has led to 14 (12.4%) patients receiving different adjuvant treatments compared with what would have been indicated if we had only taken into account the biologic status of the primary tumor. This study therefore showed that differences in biological characteristics of multifocal/multicentric lesions play a crucial role in the adjuvant treatment decision making process. In this study, we will concentrate on a larger series of patients with multifocal invasive ductal breast cancer lesions. We aim at: 1. Evaluating the incidence of multifocality according to the different breast cancer molecular subtypes (ER-/HER2-, HER2+, ER+/HER2-). 2. Evaluating the incidence of multifocality in patients with hereditary breast cancer disease (presence of germline BRCA1 or BRCA2 mutations). Moreover, we would like to investigate if multifocal lesions with BRCA1 or BRCA2 mutations exhibit a characteristic combination of substitution mutation signatures and a distinctive profile of deletions as demonstrated recently by Nik-Zainal and colleagues (9). 3. Correlating multifocality with clinical information in order to define its influence on patients? survival (DFS and OS). 4. Carrying high coverage targeted gene sequencing of driver cancer genes and genes whose mutation is of therapeutic importance in order to compare clinically-relevant genetic differences between several multifocal breast cancer lesions. 5. Evaluating the impact of the distance between the different lesions on the clinical outcome but also on the genetic differences. 6. Comparing gene expression patterns between several multifocal breast cancer lesions and correlate them with the results of the targeted genes screen. 7. Characterizing the genomic and transcriptomic status of cancer related genes in metastatic lesions (local recurrence, positive lymph node or distant metastatic sites) from the same multifocal invasive ductal breast cancer patients in order to evaluate the consequence of genomic and transcriptomic heterogeneity of multifocal lesions on metastatic lesions. Multiple (multifocal/multicentric) breast carcinomas, especially when occurring in the same breast, represent a real challenge for both pathologists and clinicians in terms of identifying the cellular origin and the best therapeutic choice. This project has the potential to identify genetic/transcriptomic differences existing between several lesions constituting multifocal breast cancers, which in the routine clinical practice are usually considered to be homogeneous among them. We foresee validating significant results in a larger series of patients and this, in turn, could have a remarkable impact on the treatment and clinical management of multifocal breast cancers. Indeed, we hope to provide some evidence whether or not each focus matters in multifocal and multicentric breast cancer to define the adequate therapeutic approach, especially in the context of targeted therapies. The work to be done at Sanger will be target gene screen pooling of 1400 samples.
Illumina HiSeq 2000
908
EGAD00001000625
The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark.
Illumina HiSeq 2000
2
EGAD00001000626
Exome sequencing data for tumor and matched normal samples of the EGAS00001000495 project.
Illumina HiSeq 2000
114
EGAD00001000627
Transcriptome sequencing data of tumor and 10 matched normal samples of the EGAS00001000495 project
Illumina HiSeq 2000
68
EGAD00001000628
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
66
EGAD00001000630
In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.
Illumina HiSeq 2000
7
EGAD00001000631
PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
4
EGAD00001000632
AB SOLiD 4 System
12
EGAD00001000634
The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize the critical secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, accounting for at least 43% of genomic rearrangements and characterized by the presence of recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction and a ten-fold enrichment at promoters and enhancers of genes actively transcribed in early B-lineage development. Single-cell tracking shows that this mechanism is not restricted to one founder cell but is rather active throughout leukemic evolution. Integration of point mutation and rearrangement data identifies recurrent inactivation of ATF7IP and MGA as two new tumor suppressor genes.Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, striking promoters and enhancers of the genes that normally control B-cell differentiation.
Illumina HiSeq 2000
2
EGAD00001000635
The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize the critical secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, accounting for at least 43% of genomic rearrangements and characterized by the presence of recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction and a ten-fold enrichment at promoters and enhancers of genes actively transcribed in early B-lineage development. Single-cell tracking shows that this mechanism is not restricted to one founder cell but is rather active throughout leukemic evolution. Integration of point mutation and rearrangement data identifies recurrent inactivation of ATF7IP and MGA as two new tumor suppressor genes.Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, striking promoters and enhancers of the genes that normally control B-cell differentiation.
Illumina Genome Analyzer II
Illumina HiSeq 2000
50
EGAD00001000636
The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize the critical secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, accounting for at least 43% of genomic rearrangements and characterized by the presence of recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction and a ten-fold enrichment at promoters and enhancers of genes actively transcribed in early B-lineage development. Single-cell tracking shows that this mechanism is not restricted to one founder cell but is rather active throughout leukemic evolution. Integration of point mutation and rearrangement data identifies recurrent inactivation of ATF7IP and MGA as two new tumor suppressor genes.Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, striking promoters and enhancers of the genes that normally control B-cell differentiation.
Illumina Genome Analyzer II
117
EGAD00001000637
Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.
Illumina Genome Analyzer II
Illumina HiSeq 2000
4
EGAD00001000638
Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.
Illumina HiSeq 2000
20
EGAD00001000639
Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.
Illumina HiSeq 2000
3
EGAD00001000640
Transcriptome studies in patients with rare genetic diseases can potentially aid in the
interpretation of likely causal genetic variation through identification of altered transcript
abundance and/or structure. RNA-Seq is the most sensitive assay for both investigating
transcript structure and abundance
The primary aim of this pilot project is to investigate to what degree integrating exome-Seq
and RNA-Seq data on the same individual can accelerate the identification of causal alleles
for rare genetic diseases. There are two main strands to this: (i) identifying which variants
discovered in exome-seq appear to be having a functional impact on transcripts, and (ii)
identifying transcript outliers, especially among known causal genes, that may not necessarily
have a causal variant identified from exome sequencing. The latter may identify the presence
of causal variants that lie far from coding regions (e.g. the formation of cryptic splice sites
deep within introns, or loss of long range regulatory elements), which can be confirmed with
further targeted genetic assays. Just over 50% of all disease-causing variants recorded in the
Human Gene Mutation Database (HGMD) affect transcript structure and abundance (e.g.
nonsense SNVs, essential splice site SNVs, frameshifting indels, CNVs).
This pilot project will study RNA from lymphoblastoid cell-lines from 12 patients with
primordial dwarfism syndromes, for 10 of these samples we have previously generate exome
data as part of our collaboration with the group of Prof Andrew Jackson. The two remaining
samples are positive controls where the causal mutation is known, and is known to affect
transcript structure and/or abundance.
Primordial dwarfism is a prime candidate for these RNA-seq studies because all known
causal mutations to date have key roles in DNA replication and thus, unsurprisingly, the
products of the causal genes are typically ubiquitously expressed.
Each RNA will be sequenced, with two technical replicates (independent RT-PCR and libraries) per
sample, and each replicate run in 1/2 of a HiSeq lane using 100bp paired reads.
Samples preparation was as follows :The cells were grown to confluency, then pellets frozen at -80. RNA samples were prepared using the Qiagen RNeasy kit, then nanodropped and analyzed using the bioanalyzer to determine concentration and purity.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
24
EGAD00001000641
DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient endometrial tumors.
Complete Genomics
Illumina HiSeq 2000
44
EGAD00001000642
Illumina HiScanSQ
2
EGAD00001000643
Illumina HiScanSQ
2
EGAD00001000644
ICGC PedBrain DNA Methylation project
Illumina HiSeq 2000
42
EGAD00001000645
ICGC MMML-seq Data Freeze July 2013 whole genome sequencing
42
EGAD00001000646
A selection of human cancers harbours somatic driver mutations in genes encoding histones, most notably childhood brain tumours with K27M substitutions of the histone 3.3 gene, H3F3A. We performed whole genome sequencing of the benign cartilage tumour, chondroblastoma, and targeted sequencing of histone 3.3 genes, H3F3A and H3F3B, in seven further skeletal tumour types. We identified an exceptionally high prevalence of novel histone 3.3 driver mutations at glycine 34 and at lysine 36. Histone 3.3 gene mutations were found in 91% in giant cell tumours of bone (48/53), mainly H3F3A G34W variants, and in 92% of chondroblastoma (73/79), predominantly K36M mutations in H3F3B. H3F3B is paralogous to the cancer gene H3F3A. However, H3F3B driver variants have not previously been reported in human cancer. Our observation demonstrate remarkable tumour-specificity of mutations, with respect to which histone 3.3 gene and residue is mutated, indicating that the advantage these mutations confer is tumour dependent. Moreover, tumour-specific mutation of H3F3A and H3F3B suggests, that although both genes encode identical proteins, they are likely non-redundant and employed differentially during skeletal development.
Illumina HiSeq 2000
14
EGAD00001000647
We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.
Illumina HiSeq 2000
110
EGAD00001000648
ICGC MMML-seq Data Freeze July 2013 transcriptome sequencing
31
EGAD00001000650
ICGC MMML-seq Data Freeze July 2013 miRNA sequencing
52
EGAD00001000652
Pulldown experiments will be performed on a number of patients with Myeloproliferative Neoplasms (MPN). The pulldown will be a bespoke design targeting known mutations, this pulldown will be sequenced and analysed to inform prevalence of mutations and to inform to the possibility of use as a diagnostic tool.
Illumina HiSeq 2000
1036
EGAD00001000653
This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.
Illumina HiSeq 2000
10
EGAD00001000654
DATA FILES FOR BALL-PAX5
Illumina HiSeq 2000
153
EGAD00001000655
DATA FILES FOR Histone-NSD2_RNASeq
Illumina HiSeq 2000
8
EGAD00001000656
FACS phenotype of 1629 Sardinian samples
1629
EGAD00001000657
DATA FILES FOR Histone Capture bams
Illumina HiSeq 2000
962
EGAD00001000658
Changes in gene dosage are a major driver of cancer1, engineered from a finite, but increasingly well annotated, repertoire of mutational mechanisms2-6. These processes operate over levels ranging from individual exons to whole chromosomes, often generating correlated copy number alterations across hundreds of linked genes. An example of the latter is the 2% of childhood acute lymphoblastic leukemia (ALL) characterized by recurrent intrachromosomal amplification of megabase regions of chromosome 21 (iAMP21)7,8 To dissect the interplay between mutational processes and selection on this scale, we used genomic, cytogenetic and transcriptional analysis, coupled with novel bioinformatic approaches, to reconstruct the evolution of iAMP21 ALL. We find that individuals born with the rare constitutional Robertsonian translocation between chromosomes 15 and 21, rob(15;21)(q10;q10)c, have ~2700-fold increased risk of developing iAMP21 ALL compared to the general population. In such cases, amplification is initiated by chromothripsis involving both sister chromatids of the dicentric Robertsonian chromosome. In contrast, sporadic iAMP21 is typically initiated by breakage-fusion-bridge (BFB) events, often followed by chromothripsis or other rearrangements. In both sporadic and iAMP21 in rob(15;21)c individuals, the final stages of amplification frequently involve large-scale duplications of the abnormal chromosome. The end-product is a derivative chromosome 21 or a derivative originating from the rob(15;21)c chromosome, der(15;21), respectively, with gene dosage optimised for leukemic potential, showing constrained copy number levels over multiple linked genes. In summary, the constitutional translocation, rob(15;21)c, predisposes to leukemia through a novel mechanism, namely a propensity to undergo chromothripsis, likely related to its dicentric nature. More generally, our data illustrate that several cancer-specific mutational processes, applied sequentially, can co-ordinate to fashion copy number profiles over large genomic scales, incrementally refining the fitness benefits of aggregated gene dosage changes.
Illumina Genome Analyzer II
Illumina HiSeq 2000
9
EGAD00001000659
Illumina HiSeq 2000
12
EGAD00001000660
Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826
353
EGAD00001000661
Bespoke validation experiments will be performed on ER+ Breast Cancer cases to confirm the presence of mutations found in whole genome sequencing.
Illumina HiSeq 2000
46
EGAD00001000662
We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found.
Illumina HiSeq 2000
46
EGAD00001000663
This study aims to re-sequence findings from whole genome studies using a bespoke pulldown method to validate mutations in those genomes sequenced.
Illumina HiSeq 2000
47
EGAD00001000664
Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009);duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA.Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa.This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads):GBM103 macroH2A1: 17x H3K36me3: 20xMB59 macroH2A1: 11x H3K36me3: 11x
7
EGAD00001000665
Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Sample derived from secondary myelodysplastic syndrome (MDS), arising after treatment for medulloblastoma in an 11-year old female Li-Fraumeni syndrome case (LFS-MB1; Rausch et al., 2012; matching WGS data available under EGAS00001000085).
1
EGAD00001000666
HSC73_clone: Bone marrow mononuclear cells from the healthy 73 years old female were thawed and labeled with Alexa-Fluor 488-conjugated anti-CD34 (581, Biolegend), Alexa-Fluor 700-conjugated anti-CD38 (HIT2, eBioscience), a cocktail of APC-conjugated lineage antibodies consisting of anti-CD4 (RPA-T4), anti-CD8 (RPA-T8), anti-CD11b (ICRF44), anti-CD20 (2H7), anti-CD56 (B159, all BD Biosciences), anti-CD14 (61D3), anti-CD19 (HIB19) and anti-CD235a (HIR2, all eBiocience) and 1 micro-gram/ml propidium iodide (Sigma). Using a BD FACSAria cell sorter, single Lin-CD34+CD38-PI- cells were individually sorted into low-adhesion 96-well tissue culture plates (Corning) containing 100micro-litre of StemSpan Serum-Free Expansion Medium (Stemcell technologies) supplemented with 100ng/ml of human SCF and FLT-3L, 50ng/ml of human TPO, 20ng/ml of human IL-3, IL-6 and G-CSF (all cytokines from Peprotech) and 50U/ml of penicillin and 50μg/ml of streptomycin (Sigma). Cells were incubated at 37 degrees C in a humidified atmosphere with 5% CO2 in air. After 5 days in culture, another 100micro litres of cytokine-containing medium were added. 13 days after seeding, clones B6 and G2 had expanded to approx. 105 cells and were selected for whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) after tagmentation-based library preparation (see Extended Experimental Procedures) for clone B6 and standard library preparation for clone G2. For germline-control ~106 unsorted bone marrow mononuclear cells from the same donor were used for sequencing. An average of 30-fold sequence coverage for each the clones and the matching control were obtained.L4clone: A progenitor cell clone was raised from a peripheral blood sample of the 39 year old healthy female. Frozen peripheral blood mononuclear cells (PBMCs) were isolated from 2 ml heparinised peripheral blood via Ficoll Paque density centrifugation. A methylcellulose assay was performed as described earlier (Weisse et al., 2012). In brief, non-adherent mononuclear cells were incubated in the presence of the recombinant human cytokines IL-3, IL-5 and GM-CSF (R&D systems) over 14 days to induce colony formation. Colonies were detected under an inverted light microscope, and plucked by a pipette when colonies had approximately 10,000 cells/CFU. Each colony was washed three times in PBS and finally frozen as a cell pellet in -80 degrees C. Genomic DNA was isolated using the QIAamp DNA micro kit according to the instructions of the manufacturer (Qiagen, Hilden, Germany). Whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) was performed for colony 4 after tagmentation-based library preparation and resulted in 15-fold sequence coverage for each the colony and the matching whole blood.
5
EGAD00001000667
Illumina HiSeq 2000
72
EGAD00001000669
High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to the emergence of treatment-resistant subclones. We sought to measure the degree of genomic diversity within primary, untreated HGSCs to examine the natural state of tumour evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on 31 spatially and temporally separated HGSC tumour specimens (six patients), including ovarian masses, distant metastases and fallopian tube lesions. We found widespread intratumoural variation in mutation, copy number and gene expression profiles, with key driver alterations in genes present in only a subset of samples (eg PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range 10.2 to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole-genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology, with common aetiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating that diversity arises at early stages of tumourigenesis. Our results revealed that HGSCs exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug-resistance mechanisms
Illumina Genome Analyzer
25
EGAD00001000670
A potential and very serious side effect of treating IBD with antiTNFa therapies (the currentgold standard) is the development of systemic lupus erythematosis (SLE). This side effect israre and unpredictable. Out of several thousand cases having received treatment, theUniversity of Calgary have accumulated 12 individuals with full phenotyping and novelserological antibody discovery panel data. We propose to exome sequence these samples inan effort to identify rare highly-penetrant variants that could be underlying this severephenotype.
Illumina HiSeq 2000
15
EGAD00001000671
Primary sclerosing chloangitis is a rare autoimmune disease of the liver (prevalence =10/100,000) with a mean age of onset of 40 years. We are currently undertaking GWASand immunochip experiments to identify loci underlying PSC susceptibility. Through ourcollaborators at the University of Calgary we have access to DNA from three parent-offspringtrios where the children required liver transplants due to PSC before the age of 9. These areextremely rare cases indeed and we believe that exome-sequencing represents a powerfulmeans of identifying the causal mutation underlying this severe phenotype.
Illumina HiSeq 2000
5
EGAD00001000672
Whole-genome Bisulfite sequencing of two multiple myeloma samples and one pooled sample of plasma cells.
Illumina HiSeq 2000
3
EGAD00001000673
WGBS-seq for monocytes and neutrophils
Illumina HiSeq 2000
12
EGAD00001000674
DNaseI-seq for monocytes
Illumina HiSeq 2000
4
EGAD00001000675
RNA-seq for monocytes and neutrophils
Illumina HiSeq 2000
12
EGAD00001000676
ChIP-seq for monocytes and neutrophils
Illumina HiSeq 2000
14
EGAD00001000677
Genome-wide analysis of H3K27me3 occupancy and DNA methylation in
K27M-mutant and H3.3-WT primary pediatric high-grade gliomas (pHGGs)
as well as pediatric pHGG cell lines. The study aims to elucidate the
connection between K27M-induced H3K27me3 reduction and changes in DNA
methylation as well as gene expression.
Illumina HiSeq 2000
19
EGAD00001000678
FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.
Illumina HiSeq 2000
341
EGAD00001000679
A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.
Illumina HiSeq 2000
107
EGAD00001000680
Single end short-read (50 bp) SOLiD 4 sequencing data for 300 individuals, constituting 100 patient-parent trios. For more details please read; http://www.nejm.org/doi/full/10.1056/NEJMoa1206524
AB SOLiD 4 System
202
EGAD00001000688
In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy.
Illumina MiSeq
25
EGAD00001000689
Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of 3 men. For each of three different prostates, multiple tumour samples (4, 5, and 3 depending on the case) and one normal tissue sample were whole genome sequenced with a matched blood sample using the Illumiuna HiSeq platform. Tumour samples were sequenced to a target depth of 50X and normals and blood to a target depth of 30X.
As of September 2020, some of the studies using these data include:
Cooper et al, Nature Genetics 2015 (PMID: 25730763)
Wedge et al, Nature Genetics 2018 (PMID: 29662167)
Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)
Illumina HiSeq 2000
-
EGAD00001000691
Dataset for "Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability"
12
EGAD00001000692
Files associated with the dataset: HS1626.bam, HS1484.bam, HS1483.bam, HS1482.bam, HS1481.bam, HS1480.bam, HS1479.bam, HS1478.bam, A13805.bam, A13800.bam, A13799.bam, A05253.bam, A05252.bam, A13806.bam
Illumina Genome Analyzer
Illumina Genome Analyzer II
Illumina HiSeq 2000
12
EGAD00001000693
The genetic consequences of cellular transformation by Epstein-Barr-Virus were assessed by comparing whole genome sequences of the original genome (before transformation) and the genome after transformation.
2
EGAD00001000694
This is an ongoing project and continuation to all the sequencing we have been doing over the last few years. We have some additional families and probands with syndromes of insulin resistance not previously sequenced within uk10k or other core funded projects. We would like to complete the sequencing in all of the good quality families and probands we have, this would require another ~50 samples to be WES sequenced. This cohort has already proven to be a rich source of interesting findings with papers in Science and Nature genetics.
Illumina HiSeq 2000
68
EGAD00001000695
DATA FILES FOR SJLGG
Illumina HiSeq 2000
46
EGAD00001000696
The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.
This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.
The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.
Illumina HiSeq 2000
5
EGAD00001000697
Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
90
EGAD00001000698
Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.The whole exome sequencing data of 20 SHH medulloblastomas from phs000504.v1.p1 dataset has been used in our study on SHH medulloblastomas: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000504.v1.p1
4
EGAD00001000699
Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.
Illumina HiSeq 2000
78
EGAD00001000702
Complete set of bam files associated with study EGAS00001000622
190
EGAD00001000703
SCLC - Whole genome sequencing data
Publication Peifer et al., 2012, Nature Genetics
Illumina Genome Analyzer IIx
29
EGAD00001000704
Illumina HiSeq 2000
-
EGAD00001000705
Whole genome sequencing of 20 tumour and normal pairs of diffuse intrinsic pontine glioma (DIPG)
Illumina HiSeq 2000
40
EGAD00001000706
Whole exome sequencing of 6 tumour and normal pairs of diffuse intrinsic pontine glioma (DIPG)
Illumina HiSeq 2000
12
EGAD00001000707
Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma by massively-parallel sequencing of tumour samples. Comparison of genomic characteristics of pretreatment 'sensitive' to recurrence 'resistant' tumours to identify the genetics of drug resistance.
Illumina HiSeq 2000
57
EGAD00001000708
AZIN1 amplicon sequencing data of the EGAS00001000495 project.
454 GS FLX Titanium
69
EGAD00001000709
Dataset of CageKid Blood DNA samples
95
EGAD00001000710
Whole Genome Bisulfite-seq of four B cell samples
Illumina HiSeq 2000
4
EGAD00001000711
Illumina HiSeq 2000
42
EGAD00001000712
Illumina HiSeq 2000
72
EGAD00001000713
Illumina HiSeq 2000
12
EGAD00001000714
102
EGAD00001000715
Exome sequencing was performed for paired tumor/normal samples from patients with corticotropin-independnet Cushing's syndrome. Tumor DNA was extracted from adrenocortical adenomas and normal DNA was extracted from adjacent adrenal tissues or periphral blood.
Illumina HiSeq 2000
16
EGAD00001000716
RNAseq data, Publication Fernandez-Cuesta et al., 2014, CD74-NRG1 fusions in lung adenocarcinoma
Illumina HiSeq 2000
25
EGAD00001000717
Dataset of CageKid Tumor DNA samples
95
EGAD00001000718
Dataset of CageKid Tumor RNA samples
91
EGAD00001000719
Dataset of CageKid Normal RNA samples
45
EGAD00001000720
Dataset of CageKid tumor-normal paired RNA samples
90
EGAD00001000721
This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.
Illumina HiSeq 2000
20
EGAD00001000722
Extension of angiosarcoma whole genome sequencing study
Illumina HiSeq 2000
8
EGAD00001000723
Relative Spatial Homogeneity of Embryonal Brain Tumors of Childhood
42
EGAD00001000724
Illumina HiSeq 2000
68
EGAD00001000725
This dataset contains RNA sequencing data for 675 cancer cell lines. RNA libraries were made with the TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer protocol. The libraries were sequenced on an Illumnia HiSeq 2000
Illumina HiSeq 2000
675
EGAD00001000726
In total 30 Acute Myeloid Leukemias with an acquired inv(3)(q21q26) or t(3;3)(q21;q26) have been characterized by whole transcriptome sequencing (RNA-Seq). The 3q-aberration leads to overexpression of the proto-oncogene EVI1, but the mechanism of overexpression has thus far been elusive. The RNA-Seq was integral in determining the precise enhancer inducing the overexpression and led to other key discoveries.
Illumina HiSeq 2500
30
EGAD00001000727
Targeted resequencing on the specific regions chr3:126036241-130672290 and chr3:157712147-175694147 in hg19 centered on the chromosomal regions 3q21 and 3q26 respectively. The focus lies on the detection of the exact breakpoints in Acute Myeloid Leukemia (AML) patients having acquired a inv(3)(q21q26) or t(3;3)(q21;q26). This dataset contains all information to detect all structural variants contained within these regions, including the 3q-aberrations inducing the overexpression of the proto-oncogene EVI1.
Illumina HiSeq 2500
38
EGAD00001000728
Low coverage whole genome sequencing of samples from individuals from Friuli Venezia Giulia, an Italian genetic isolate population.
Illumina HiSeq 2000
199
EGAD00001000729
The Val Borbera is a region characterized by low iodine and high prevalence of thyroid disorders, the commonest endocrine disorders in the general population. About 30% of the participants of the Val Borbera Project were affected by such disorders and were characterized by several parameters, TSH level, anti TPO antibodies, echography, family origin. Individuals with extreme phenotypes were identified and could be clustered based on family origin and genotype.
We propose to exome sequence 6 of them, affected with true goiter, at high dept (40-60x) to obtain information on exonic rare variants. Due to the family structure and to the availability of whole genome sequence information on 110 individuals from the isolated population we expect to be able to identify putative causative variants for thyroid disorders that may be studied in the remaining affected individuals.
Illumina HiSeq 2000
8
EGAD00001000730
The VBSEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Up to 100 Val Borbera samples will be sequenced to a 6x depth.
Illumina HiSeq 2000
110
EGAD00001000731
This study includes Phase 2 whole-genome sequencing data (at 4x depth)of 100 individuals from an Italian genetic isolate population (Val Borbera, abbreviated VBI) of the Italian Network of Genetic Isolates (INGI). The INGI-VBI_SEQ2 project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.
Illumina HiSeq 2000
100
EGAD00001000732
RNA sequencing to validate findings of somatic pseudogenes acquired during cancer development
Illumina HiSeq 2000
3
EGAD00001000733
The dataset entails 48 RRBS libraries of 24 siblings. 24 individuals are conceived during the Dutch Famine, a severe 6 month famine at the end of World War 2. A same sex sibling was added as a control, allowing partial matching for (early) familial environment and genetics.
Illumina Genome Analyzer IIx
48
EGAD00001000734
Paired end Illumina sequencing of whole exomes of multiple tumour regions.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
Illumina HiSeq 2500
88
EGAD00001000735
Here we present the genomes of three secondary angiosarcomas
Illumina HiSeq 2000
7
EGAD00001000737
Whole exome sequencing data from 30 donors (46 tumors and 30 non-tumoral whole exome sequencing, paired-end, HiSeq 2000, Illumina) collected by the Inserm U674, PI Jessica Zucman-Rossi - Institut National du Cancer (INCa), PI Fabien Calvo, France.
Illumina HiSeq 2000
76
EGAD00001000738
Extension of angiosarcoma whole genome sequencing study
Illumina HiSeq 2000
4
EGAD00001000740
UK10K_COHORT_ALSPAC REL-2012-06-02: Low-coverage whole genome sequencing; variant calling, genotype calling and phasing
Illumina HiSeq 2000
2307
EGAD00001000741
UK10K_COHORT_TWINSUK REL-2012-06-02: Low-coverage whole genome sequencing; variant calling, genotype calling and phasing
Illumina Genome Analyzer II
Illumina HiSeq 2000
1854
EGAD00001000743
These files contain a total of 20.4M SNVs and the complete information output by the GATK UnifiedGenotyper v1.4 on all 767 GoNL samples. These calls are not trio-aware and all genotypes were reported regardless of their quality. Both filtered and passing calls are reported in these files. Filtered calls include (1) calls failing our VQSR threshold and (2) calls in the GoNL inaccessible genome.
-
EGAD00001000744
The samples in this panel come from 250 families: 248 parents-child trios and 2 parent-child duos. As the children do not provide additional haplotypes or population information, they were excluded from the panel. The samples present in the release are composed of 248 couples, 2 single individuals and 1 sample composed from the 2 haplotypes from the duo's children transmitted by their missing parent. The composed sample is named gonl-220c_223c.The files contain a total of 18.9M SNVs and 1.1M INDELs in autosomal chromosomes. They were generated by phasing/imputing the SNVs (a) and INDELs (b) using MVNCall. Only sites passing filters are reported. Sites filtered as part of the GoNL inaccessible genome were kept (but flagged as filtered) and still may contain true positive calls but should be used with care as they are located in parts of the genome that are less well captured (systematic under or over-covered or low-mapping quality)
-
EGAD00001000745
Data supporting the paper Transcriptional diversity during lineage commitment of human blood progenitors
Illumina HiSeq 2000
PacBio RS
26
EGAD00001000746
Fernandez-Cuesta et al., RNAseq data Pipline
Illumina HiSeq 2000
25
EGAD00001000747
Genomic libraries will be generated from total genomic DNA derived from 4000 samples with Acute Myeloid Leukaemia. Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 64 Samples will be individually barcoded and subjected to up to one lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.
Illumina HiSeq 2000
2734
EGAD00001000748
In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy.
Illumina MiSeq
19
EGAD00001000749
Illumina HiSeq 2000
12
EGAD00001000750
UK10K_RARE_FIND REL-2013-10-31 variant calling
Illumina HiSeq 2000
1151
EGAD00001000752
UK10K_RARE_CILWG REL-2013-09-09
Illumina HiSeq 2000
4
EGAD00001000753
UK10K_RARE_FINDWG REL-2013-09-09
Illumina HiSeq 2000
4
EGAD00001000754
UK10K_RARE_NMWG REL-2013-09-09
Illumina HiSeq 2000
5
EGAD00001000755
UK10K_OBESITY_GS UK10K_EXOME_EXTRAS
Illumina HiSeq 2000
5
EGAD00001000756
UK10K_OBESITY_SCOOP UK10K_EXOME_EXTRAS
Illumina HiSeq 2000
1
EGAD00001000757
UK10K_RARE_SIR UK10K_EXOME_EXTRAS
Illumina HiSeq 2000
2
EGAD00001000758
dataset for BGI bladder cancer project
Illumina Genome Analyzer II
198
EGAD00001000759
Illumina HiSeq 2000
86
EGAD00001000760
dataset for esophageal cancer, 17 pairs for whole-genome sequencing and 71 pairs for whole-exome sequencing
Illumina HiSeq 2000
176
EGAD00001000761
In order to establish copy number profiles from the various samples we prepared libraries and subjected them to whole-genome sequencing at a shallow sequencing depth (0.1x)
Illumina MiSeq
14
EGAD00001000762
We utilized exome sequencing for DNA obtained from saliva (germline DNA) and the four spatially separated tumor foci and 3 corresponding lymph node metastases
Illumina HiSeq 2000
8
EGAD00001000763
We used targeted deep sequencing to accurately establish the allele frequencies of the mutations identified by exome sequencing
Illumina MiSeq
23
EGAD00001000764
Adrenocortical carcinomas (ACC) are aggressive cancers originating in the cortex of the adrenal glands. Despite the overall poor prognosis, ACC outcome is heterogeneous. CTNNB1 and TP53 mutations are frequent in these tumors, but the complete spectrum of genetic changes remains undefined. Exome sequencing and SNP array analysis of 45 ACC revealed recurrent alterations in known drivers (CTNNB1, TP53, CDKN2A, RB1, MEN1) and genes not previously reported to be altered in ACC (ZNRF3, DAXX, TERT and MED12), which were validated in an independent cohort of 77 ACC. The cell-surface transmembrane E3 ubiquitin ligase ZNRF36 was the gene the most frequently altered (21%), and appears as a potential novel tumor suppressor gene related to the ß-catenin pathway.Our integrated genomic analyses led to the identification of two distinct molecular subgroups with opposite outcome. The C1A group of poor outcome ACC was characterized by numerous mutations and DNA methylation alterations, whereas the C1B group with good prognosis displayed a specific deregulation of two miRNA clusters. Thus, aggressive and indolent ACC correspond to two distinct molecular entities, driven by different oncogenic alterations.
Illumina HiSeq 2000
45
EGAD00001000774
This study includes whole-genome sequencing data (at 4x depth) of 100 individuals from an Italian genetic isolate population (Carlantino, abbreviated CARL) of the Italian Network of Genetic Isolates (INGI). The INGI-CARL_SEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.
Illumina HiSeq 2000
106
EGAD00001000775
Whole exome sequencing of 41 melanomas and normal DNA from Braf mutant mice: 15 tumours from UV exposed mice, 15 tumours from non-exposed mice and 11 from UV exposed, sunscreen-protected mice.
Illumina HiSeq 2000
80
EGAD00001000776
UK10K_COHORT_IMPUTATION REL-2012-06-02: imputation reference panel (20140306); Merged UK10K+1000Genomes Phase 3 imputation reference panel added (20160420)
Illumina Genome Analyzer II
Illumina HiSeq 2000
3781
EGAD00001000777
Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients.
16
EGAD00001000779
AB SOLiD 4 System
2
EGAD00001000780
Illumina HiSeq 2000
18
EGAD00001000781
Whole genome, high coverage, sequencing of 128 Ashkenazi Jewish controls
128
EGAD00001000782
Whole-genome sequencing was performed by Illumina Inc (San Diego, CA). Libraries were constructed with ~300bp insert length and paired-end 100bp reads were sequenced on Illumina HiSeq2000.
Illumina HiSeq 2000
190
EGAD00001000783
Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50 ). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.
Illumina HiSeq 2000
Illumina HiSeq 2500
400
EGAD00001000784
This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.
Illumina HiSeq 2000
242
EGAD00001000785
We propose to definitively characterise the somatic genetics of a selection of rare bone cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.
Illumina HiSeq 2000
33
EGAD00001000786
We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient.
Illumina MiSeq
1
EGAD00001000789
UK10K_COHORT_ALSPAC REL-2012-06-02: Phenotype data
1927
EGAD00001000790
UK10K_COHORT_TWINSUK REL-2012-06-02: Phenotype data
1854
EGAD00001000791
Exome sequencing of familial and sporadic small cell cancer of ovary cases.
Illumina HiSeq 2000
Illumina HiSeq 2500
16
EGAD00001000792
Whole exome sequencing of paediatric glioblastoma with mutations reported in the manuscript: Mutations in ACVR1, FGFR1 and TP53 associate with tumor location in histone H3 K27M pediatric midline high-grade astrocytoma
Illumina HiSeq 2000
Illumina HiSeq 2500
38
EGAD00001000794
Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis.
Illumina HiSeq 2000
11
EGAD00001000795
Fernandez-Cuesta et al, 2014, Nature Communication, RNA Sequencing data set
Illumina HiSeq 2000
69
EGAD00001000796
This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected in Leuven in collaboration with Koen Devriendt. Ethic approval has been sought for in Leuven, Belgium and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina).
Illumina HiSeq 2000
167
EGAD00001000797
This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected at the Royal, Brompton Hospital in collaboration with Stuart Cook and Piers Daubeney. Ethic approval has been sought for in the UK and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina).
Illumina HiSeq 2000
48
EGAD00001000798
In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unclear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types.
Illumina HiSeq 2000
Illumina HiSeq 2500
Illumina MiSeq
28
EGAD00001000799
The exome sequencing is performed using Agilent SureSelect 50Mb exome v3 and Hiseq 75bp paired reads with an mean sequencing coverage target of 50X.
Illumina HiSeq 2000
95
EGAD00001000800
This project aims to study exomes from families and trios with
congenital heart disease (CHD). The samples have been collected under
the Competence Network - Congenital Heart Defects in Berlin, Germany.
The phenotypes are mainly left ventricular outflow obstruction (aortic
stenosis, bicuspd aortic valve disease coarctation and hypoplastic
left heart), but will also include samples with hypoplastic right
heart and atrioventricular septal defects. We will perform whole exome
sequencing using Agilent sequence capture and Illumina HiSeq
sequencing.
Illumina HiSeq 2000
406
EGAD00001000802
UK10K_RARE_CILWG REL-2013-03-06
Illumina HiSeq 2000
2
EGAD00001000803
UK10K_RARE_FINDWG REL-2013-03-06
Illumina HiSeq 2000
2
EGAD00001000804
UK10K_RARE_NMWG REL-2013-03-06
Illumina HiSeq 2000
1
EGAD00001000805
UK10K_RARE_THYWG REL-2013-03-06
Illumina HiSeq 2000
2
EGAD00001000806
Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study
Illumina HiSeq 2000
63
EGAD00001000807
Whole Exome Sequencing (WES) for St. Jude High Grade Glioma (HGG) study
Illumina HiSeq 2000
148
EGAD00001000808
RIKEN collection WGS reads for 321 HCC and blood matched samples from 158 donors submitted to ICGC for release 15
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
321
EGAD00001000809
RIKEN collection WGS reads for 61 liver cancer and matched blood samples from 30 donors displaying biliary phenotype
Illumina HiSeq 2000
61
EGAD00001000810
Dataset for whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors
Illumina HiSeq 2000
106
EGAD00001000811
Whole exome sequencing of 6 HCCs and matched background liver in children with bile salt export pump deficiency.
Illumina HiSeq 2000
12
EGAD00001000812
Sequencing of 350 cancer genes in BC samples from patients treated with either Epirubicin or Paclitaxel monotherapy in the neoadjuvant setting.
Illumina HiSeq 2000
364
EGAD00001000813
Fernandez-Cuesta et al., 2014, Nature Communication,
Whole genome sequencing was performed using a read length of 2x100 bp for all
samples. On average, 110 Gb of sequence were produced per sample, aiming a
mean coverage of 30x for both tumour and matched normal.
Illumina HiSeq 2000
29
EGAD00001000814
Whole genome alignments of DIPG patients
40
EGAD00001000815
Exome-seq, RNA-Seq, SNP array profiling of gastric tumor samples.
Illumina HiSeq 2000
102
EGAD00001000816
ICGC medulloblastoma whole genome sequencing data, ICGC release 16
44
EGAD00001000817
Alternative splicing plays critical roles in differentiation, development, and cancer (Pettigrew et al., 2008; Chen and Manley, 2009). The recent identification of specific spliceosome inhibitors has generated interest in the therapeutic potential of targeting this cellular process (van Alphen et al., 2009). Using an integrated genomic approach, we have identified PRPF6, an RNA binding component of the pre-mRNA spliceosome, as an essential driver of oncogenesis in colon cancer. Importantly, PRPF6 is both amplified and overexpressed in colon cancer, and only colon cancer cells with high PRPF6 levels are sensitive to its loss. Our data clearly point to an important role for PRPF6 in colon cancer growth and suggest that a better understanding of its role in alternative splicing in colon cancer is warranted. To determine the specific alternative splice forms that PRPF6 regulates in colon cancer, we plan three experiments: 1. The first involves knocking down expression of PRPF6 in two different cancer cell lines with 3 different siRNAs, and then completing RNA-seq to determine the gene expression changes that occur relative to a non-targeting control siRNA. Because of the role for PRPF6 in pre-mRNA splicing, we especially want to quantify the changes in splice-specific forms of all genes genome-wide to identify genes whose splicing is altered upon PRPF6 knockdown. 2. The second involves immunoprecipitating PRPF6 from two different cancer cell lines and isolating any RNA that is bound to PRPF6, since PRPF6 is an RNA-binding protein. We then want to carry out RNA-seq to identify which RNA molecules co-immunoprecipitated with PRPF6. This will help us determine possible functions for PRPF6 in regulating colon cancer growth. 3. The third involves overexpressing PRPF6 in cell lines and then carrying out RNA-seq to identify any changes in splice-specific gene expression. This will allow us to determine whether increased PRPF6 expression is sufficient to drive alternative splicing changes.
Illumina HiSeq 2000
34
EGAD00001000818
Quiescent Sox2+ cells drive hierarchical growth and relapse in Sonic hedgehog subgroup medulloblastoma
4
EGAD00001000819
We are aiming to investigate repair of a double strand break (DSB) within the genome in the presence and absence of the BLOOM protein. Zinc Finger Nucleases introduce DSBs at specified loci within the genome. Using sequencing we will assess the size of the deletion following repair.
Protocol
1. Transfect normal and BLOOM deficient human iPS cells with ZFNs, using AMXA
2. Harvest cells after 5 days
3. Perform column extraction of DNA
4. PCR-amplify the ZFN region
5. Sequence and analyse repair of the DSB
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
6
EGAD00001000820
Fernandez-Cuesta et al, 2014, Nature Communication, Whole exome sequencing data set
Illumina HiSeq 2000
15
EGAD00001000821
Raw sequencing data for all samples in fastq format.
Illumina HiSeq 2000
767
EGAD00001000822
Whole exome sequencing and miRNA-seq data of PPB.
Illumina HiSeq 2000
Illumina MiSeq
18
EGAD00001000824
RNA sequencing will be undertaken to reconstruct rearrangements at level of transcription to determine pathogenomic genomic events in chondromyxoid fibroma.
Illumina HiSeq 2000
1
EGAD00001000825
This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.
Illumina HiSeq 2000
454
EGAD00001000826
We propose to definitively characterise the somatic genetics of Osteosarcoma cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome and transcriptome sequencing.
Illumina HiSeq 2000
10
EGAD00001000827
n order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The methylation status of these iPS cells will be compared.
Protocol:
Primary cell cultures were generated and reprogrammed to iPS cells. DNA was extracted and immunoprecipitated using anti-methyl cytosine and anti-hydroxymethyl cytosine antibodies.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
4
EGAD00001000828
Fibroblasts have been shown to re-program into induced pluripotent stem (hiPS) cells, through over-expression of pluripotency genes. These hiPS cells show similar characteristics to embryonic stem cells including cell surface markers, epigenetic changes and ability to differentiate into the three germ layers. However it is unclear as to the extent of changes in gene expression through the re-programming process.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
6
EGAD00001000829
Illumina HiSeq 2000
16
EGAD00001000830
Illumina HiSeq 2000
14
EGAD00001000831
Illumina HiSeq 2000
30
EGAD00001000832
Illumina HiSeq 2000
16
EGAD00001000833
Illumina HiSeq 2000
10
EGAD00001000834
Illumina HiSeq 2000
20
EGAD00001000835
Illumina HiSeq 2000
8
EGAD00001000836
Illumina HiSeq 2000
49
EGAD00001000842
RIKEN collection WGS reads for 100 HCC and matched blood samples from 50 donors submitted to ICGC for release 16
Illumina HiSeq 2000
100
EGAD00001000843
Illumina HiSeq 2000
12
EGAD00001000844
Illumina HiSeq 2000
22
EGAD00001000845
44
EGAD00001000847
Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive disorder characterized by exocrine pancreatic insufficiency, bone marrow dysfunction, leukemia predisposition, and skeletal abnormalities. We aim to characterise the structural effects of SDS in patients with this disorder by exome sequencing.
Illumina HiSeq 2000
2
EGAD00001000848
To evaluate the presence of mutations in frequently mutated genes in MPN by performing targeted resequencing of a selected gene panel comprising of 111 genes across 40 samples with MPN.
Illumina MiSeq
48
EGAD00001000849
Illumina HiSeq 2000
50
EGAD00001000850
Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis.
Illumina HiSeq 2000
19
EGAD00001000853
DATA FILES FOR SJEPD
Illumina HiSeq 2000
37
EGAD00001000854
DATA FILES FOR SJEPD
Illumina HiSeq 2000
77
EGAD00001000856
Illumina HiSeq 2000
1
EGAD00001000865
WGS of 14 paired samples of Bladder Cancer patient
Illumina HiSeq 2000
28
EGAD00001000868
FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.
Illumina HiSeq 2000
Illumina HiSeq 2500
60
EGAD00001000869
It is the ambition of the team formed by members of the Netherlands Cancer Institute (NKI) and the Cancer Genome Project at the Wellcome Trust Sanger Institute (WTSI) to unravel the genomic and phenotypic complexity of human cancers in order to identify optimal drug combinations for personalized cancer therapy. Our integrated approach will entail (i) deep sequencing of human tumours and cognate mouse tumours; (ii) drug screens in a 1000+ fully characterized tumour cell line panel; (iii) high-throughput in vitro and in vivo shRNA and cDNA drug resistance and enhancement screens; (iv) computational analysis of the acquired data, leading to significant response predictions; (v) rigorous validation of these predictions in genetically engineered mouse models and patient-derived xenografts. This integrated effort is expected to yield a number of combination therapies and companion-diagnostics biomarkers that will be further explored in our existing clinical trial networks.
Illumina HiSeq 2000
62
EGAD00001000870
Testing logistics and infrastructure of molecular screening program. Core biopsies taken from invasive recurrent or metastatic breast cancer to evaluate and identify molecular traits rendering them suitable for clinical trials
Illumina HiSeq 2500
52
EGAD00001000871
The purpose of this study is to sequence 500 known cancer genes in 960 newly diagnosed high risk breast cancer patients treated with current standard of care therapies and trastuzumab, for somatic alteration and copy number changes. We will be using next gen sequencing technology to determine the prognostic relevance of these somatic genetic alterations and of teh low frequency events to determine if they are associated with trastuzumab benefit or HER2 positive breast cancer, i.e. treatment interaction. The samples will be analysed adn correlated with clinical variables including outcome.
Illumina HiSeq 2000
993
EGAD00001000872
These samples are to be analysed with the CGP Developed cancer panel and the results will be compared with WGS data from 4 different comercial providers.
Illumina HiSeq 2500
8
EGAD00001000873
Fastq files of 10 samples of condrosarcoma
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
10
EGAD00001000874
Indel/point mutation of chondrosarcoma
10
EGAD00001000875
The CRO7 clinical trial recruited patients with clinically operable rectal adenocarcinoma. Patients were randomized to either pre-operative short course surgery followed by chemo-radiotherapy only in those patients at high risk of local relapse. Patients in both arms the received standard %-FU based adjuvant chemotherapy as per local policy. We intend to use FFPE derived DNA from the primary tumours to identify patterns of mutations or copy number alterations that are predictive of local or distant relapse.
Illumina HiSeq 2000
330
EGAD00001000876
Illumina HiSeq 2000
98
EGAD00001000877
Complete WGS and RNA-Seq dataset for Australian ICGC ovarian cancer sequencing project 2014-07-07, representing 93 donors.
Sequencing was performed on Illumina HiSeq.
Alignment of the lane-level fastq data was performed with bwa (WGS data) and RSEM (transcriptome data).
For this dataset lane-level .bam files have been merged and de-duplicated to create a single bam file for each sample type (tumour/normal) for each donor.
This dataset supersedes all previous datasets for this study.
2016-08-08 updated with 14 outstanding RNA-seq samples & corresponding RSEM bams
2016-12-07 updated with 7 outstanding RNA-seq controls and corresponding RSEM bams
331
EGAD00001000878
RNA-Seq files accompanying Genetic landscape of pediatric Rhabdomyosarcoma
Illumina HiSeq 2000
42
EGAD00001000879
Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.
Illumina HiSeq 2500
335
EGAD00001000880
Genotyping by array and Transcriptome profiling by high-throughput sequencing
233
EGAD00001000881
RNA sequencing of Resistant BCC samples.
Illumina HiSeq 2000
11
EGAD00001000882
Targeted genome sequences of the human X chromosome in 4 colorectal adenomas and 4 matched normal tissues from male patients
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
8
EGAD00001000883
Illumina HiSeq paired-end exome sequencing of a trio and singleton.
Illumina HiSeq 2000
4
EGAD00001000884
In order to elucidate whether newly acquired genetic alterations during serial transplantation of patient derived primary pancreatic cancer cultures contribute to the observed clonal dynamics in vivo, all coding genes of two patient derived primary cultures and derived genetically marked serial xenografts (1°/2°/3°) were sequenced.
Illumina HiSeq 2000
10
EGAD00001000885
Exome read sequences for 30 tumor-normal pairs for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma".
Illumina HiSeq 2000
60
EGAD00001000886
RNA-Sequencing data (raw read sequences) for 23 samples, from 12 patients, for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma"
Illumina HiSeq 2000
23
EGAD00001000887
Exome sequencing of Resistant BCC samples.
Illumina HiSeq 2000
23
EGAD00001000888
NSCLC WGS.
AB 5500 Genetic Analyzer
4
EGAD00001000889
NSCLC targeted.
Ion Torrent PGM
4
EGAD00001000891
To characterize the subclonal genomic architecture of androgen-deprived metastatic prostate cancer, we performed whole-genome sequencing (WGS) of 51 tumours from 10 patients to an average sequencing depth of 55x, including multiple metastases from different anatomic sites in each patient
and, in five cases, the prostate tumour. Noncancerous DNA from blood or other tissue is used as reference comparison for each patient. The patients are part of PELICAN (Project to ELIminate Lethal Cancer) rapid autopsy study led by G. Steven Bova at Johns Hopkins University (USA) and Tampere University (Finland). As of September 2020, some of the studies using these data include: Gundem et al, Nature 2015 (PMID: 25830880). Additional EGAD00001000891 sample metadata is contained in Supplementary Information in this report.Tubio et al, Science 2014 (PMID: 25082706) Behjati et al, Nature Comm 2015 (PMID: 27615322) Wedge et al, Nature Genetics 2018 (PMID: 29662167)Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)Rodriguez-Martin et al, Nature Genetics 2020 (PMID: 32024998)Woodcock et al, Nature Comm 2020 (In Press)
Illumina HiSeq 2000
62
EGAD00001000892
Whole Genome Sequencing Illumina HiSeq data from 20 men with prostate cancer. 20 samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). These were submitted for use in the ICGC Pan-Cancer Analysis of Whole Genomes project.
Same raw data submitted in EGAD00001001116.
As of September 2020, some of the studies using these data include:
Wedge et al, Nature Genetics 2018 (PMID: 29662167)
Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)
Illumina HiSeq 2000
40
EGAD00001000893
HipSci - Healthy Normals - Exome Sequencing - May 2014
Illumina HiSeq 2000
15
EGAD00001000894
SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.
Illumina HiSeq 2500
64
EGAD00001000896
Illumina HiSeq 2000
12
EGAD00001000897
HipSci - Healthy Normals - RNA Sequencing - May 2014
Illumina HiSeq 2000
22
EGAD00001000898
Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant.
Illumina HiSeq 2000
42
EGAD00001000899
We propose to definitively characterise the somatic genetics of Metastatic breast cancer through generation of comprehensive catalogues of somatic mutations in Metastatic breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
41
EGAD00001000900
Multi-region Illumina whole-exome and/or whole-genome sequencing on tumor regions collected from early-stage NSCLC patients who underwent definitive surgical resection prior to receiving adjuvant therapy.Detected variants were validated on Ion AmpliSeq™ Custom Panel and/or Comprehensive Cancer Gene Panels.Patients covered by this dataset: L001, L002, L003, L004, L008 and L011.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
Illumina HiSeq 2500
Ion Torrent PGM
28
EGAD00001000901
The dataset includes the whole exome sequencing data from32 pairs of gallbladder caner tissues and patient-matched normal tissues.
Illumina HiSeq 2500
64
EGAD00001000902
The dataset includes the targeted gene sequencing data from51 pairs of gallbladder caner tissues and patient-matched normal tissues.
Illumina HiSeq 2500
102
EGAD00001000903
RNA-Seq data for 4 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 22 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
4
EGAD00001000904
RNA-Seq data for 7 mature neutrophil sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
7
EGAD00001000905
DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
5
EGAD00001000906
ChIP-Seq data for 1 mature eosinophil sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
1
EGAD00001000907
RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001000908
RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001000909
Bisulfite-Seq data for 1 erythroblast sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000910
Bisulfite-Seq data for 1 precursor lymphocyte of B lineage sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000911
RNA-Seq data for 4 erythroblast sample(s). 22 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
4
EGAD00001000912
RNA-Seq data for 1 CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001000913
ChIP-Seq data for 9 CD14-positive, CD16-negative classical monocyte sample(s). 59 run(s), 55 experiment(s), 55 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
9
EGAD00001000914
Bisulfite-Seq data for 3 inflammatory macrophage sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
3
EGAD00001000915
RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
4
EGAD00001000916
ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
1
EGAD00001000917
Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000918
RNA-Seq data for 3 common lymphoid progenitor sample(s). 15 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001000919
RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001000920
Bisulfite-Seq data for 1 alternatively activated macrophage sample(s). 10 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000921
Bisulfite-Seq data for 1 CD8-positive, alpha-beta T cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000922
RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001000923
Bisulfite-Seq data for 1 macrophage sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000924
ChIP-Seq data for 2 erythroblast sample(s). 14 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
2
EGAD00001000925
ChIP-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 21 run(s), 21 experiment(s), 21 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
3
EGAD00001000926
DNase-Hypersensitivity data for 2 inflammatory macrophage sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
2
EGAD00001000927
Bisulfite-Seq data for 1 Plasma cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000928
RNA-Seq data for 7 CD14-positive, CD16-negative classical monocyte sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
7
EGAD00001000929
ChIP-Seq data for 1 macrophage sample(s). 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
1
EGAD00001000930
ChIP-Seq data for 7 mature neutrophil sample(s). 68 run(s), 50 experiment(s), 50 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
7
EGAD00001000931
DNase-Hypersensitivity data for 1 macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
1
EGAD00001000932
Bisulfite-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000933
RNA-Seq data for 1 macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001000934
Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
2
EGAD00001000935
Bisulfite-Seq data for 6 mature neutrophil sample(s). 79 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
6
EGAD00001000936
ChIP-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 13 run(s), 13 experiment(s), 13 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
2
EGAD00001000937
RNA-Seq data for 1 alternatively activated macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001000938
ChIP-Seq data for 4 alternatively activated macrophage sample(s). 29 run(s), 28 experiment(s), 28 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
4
EGAD00001000939
RNA-Seq data for 3 hematopoietic stem cell sample(s). 8 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001000940
ChIP-Seq data for 3 inflammatory macrophage sample(s). 21 run(s), 21 experiment(s), 21 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
3
EGAD00001000941
Bisulfite-Seq data for 6 CD14-positive, CD16-negative classical monocyte sample(s). 86 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
6
EGAD00001000942
DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
1
EGAD00001000943
Bisulfite-Seq data for 1 germinal center B cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001000944
Whole Genome Sequencing of 5 acral melanomas and matched normal samples
Illumina HiSeq 2000
10
EGAD00001000945
NGS of 10 mucosal melanomas:Whole genome sequencing of 5 mucosal melanomas and matched normal DNAWhole exome sequencing of 5 mucosal melanomas and matched normal DNA
Illumina HiSeq 2000
20
EGAD00001000946
Divergent clonal selection dominates medulloblastoma at recurrence
125
EGAD00001000947
Genomic libraries (500 bps) will be generated from total genomic DNA derived from Colorectal cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.
Illumina HiSeq 2000
45
EGAD00001000948
A comparison of the somatic variation present in a primary colorectal tumour and three different liver metastases from the same patient.
Illumina HiSeq 2000
6
EGAD00001000949
Validations of variants identified by exome sequencing in sequential samples derived after treatment cycle with AZA.
Illumina HiSeq 2000
170
EGAD00001000950
Whole genome sequencing data for ependymomas (5 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).
10
EGAD00001000951
Whole exome sequencing data for ependymomas (42 tumor-control pairs). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).
84
EGAD00001000952
DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4)
Illumina HiSeq 2000
8
EGAD00001000963
Exome sequencing of sporadic schwannomatosis patients
16
EGAD00001000964
Low-coverage whole genome sequencing of sporadic schwannomatosis patients
16
EGAD00001000965
Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant.
Illumina HiSeq 2000
331
EGAD00001000966
Whole genome bisulfite sequencing data for 6 ependymomas plus 3 fetal controls (f1, f2, f4) and 3 adult controls (a2, a3, a4). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).
Illumina HiSeq 2000
14
EGAD00001000967
This dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis.
Illumina HiSeq 2000
4
EGAD00001000972
Whole Genome Sequencing to track subclonal heterogeneity in 18 samples from 3 Chronic Lymphocytic Leukemia patients subjected to repeated cycles of therapy. NOTE: There are only 12 BAM files available to download. The other 6 files are missing.
Illumina HiSeq 2500
18
EGAD00001000973
Van Hippel-Lindau syndrome multi-region exome sequencing of two patients
Illumina HiSeq 2000
21
EGAD00001000974
High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to emergence of treatment-resistant sub-clones. We sought to measure the degree of genomic diversity within primary, untreated HGSC to examine the natural state of tumor evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on thirty-one spatially and temporally separated HGSC tumor specimens (six patients) including ovarian masses, distant metastases, and fallopian tube lesions. We found widespread intra-tumoral variation in mutation, copy number, and gene expression profiles, with key driver alterations in genes present in only a subset of samples (e.g. PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range: 10.2% to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology with common etiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating diversity arises at early stages of tumorigenesis. Our results reveal that HGSC exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug resistance mechanisms.
Illumina HiSeq 2000
Illumina MiSeq
131
EGAD00001000975
65 prostate cancer cases transcriptome sequencing
Illumina HiSeq 2000
130
EGAD00001000976
WGS DATA FILES FOR SJPhLike
Illumina HiSeq 2000
80
EGAD00001000977
WGS dataset LCNEC study
Illumina HiSeq 2000
11
EGAD00001000978
Multi-region whole genome sequencing of an high grade serous ovarian carcinoma sample for characterization of genomic intra-tumoural heterogeneity.
Illumina HiSeq 2000
48
EGAD00001000979
We are developing a protocol to differentiate mouse and human induced pluripotent stem (IPS) and embryonic stem (ES) cells towards the haematopoietic pathway to generate erythrocytes in vitro. This system has many applications such as the study of the role of specific genes and human polymorphisms in infectious diseases such as malaria, as well as haematological diseases such as myelodysplastic syndrome. The nature of the in vitro differentiation process means that a heterogeneous population of cells is generated. In order to understand the types of cells produced with our protocol, we have performed a single cell analysis, which has the power to reveal the different populations of cells and their characteristics. For this, a cDNA library has been made that needs to be sequenced to obtain the gene expression profiles of the different cells. With this information we will be able to assess the quality of the differentiation protocol and improve it in order to produce better cells for the downstream applications.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2500
192
EGAD00001000980
This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines.
Illumina MiSeq
144
EGAD00001000983
65 prostate cancer cases wgs sequencing
Illumina HiSeq 2000
10
EGAD00001000984
This is the Whole Exome Sequencing (WES) data from 59 samples from 11 patients with lung adenocarcinomas including 48 tumor samples and 11 peripheral white blood cell samples
Illumina HiSeq 2000
59
EGAD00001000985
This is the targeted capture deep sequencing (TCS) data for validation of the mutations discovered in the WES step. There are 58 bam files of TCS data including 48 tumor samples and 10 peripheral blood WBC samples.
Illumina HiSeq 2000
58
EGAD00001000986
Pheochromocytomas and paragangliomas (PCC/PGL) are neural crest derived tumors with a very strong genetic component. We report the first integrated genomic portrayal of a large collection of PCC/PGL. SNP array analysis revealed distinct copy-number patterns associated with genetic background. Whole-exome sequencing showed a low mutation rate of 0.3 mutations per megabase, with few recurrent somatic mutations in genes not previously associated with PCC/PGL. DNA methylation arrays and miRNA sequencing identified DNA methylation changes and miRNA expression clusters strongly associated with mRNA expression profiling. Overexpression of the miRNA cluster 182/96/183 was specific of SDHB-mutated tumors and induced invasive traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster appeared as a potential driver in a subgroup of sporadic tumors. Altogether, the complete genomic landscape of PCC/PGL is mainly driven by distinct germline and/or somatic mutations in susceptibility genes and reveals different molecular entities, characterized by a set of unique genomic alterations.
Illumina HiSeq 2000
60
EGAD00001000987
Whole exome sequencing data from tumor and normal samples from carcinosarcoma (malignant mixed mullerian tumor) patients
Illumina HiSeq 2000
44
EGAD00001000988
Validation/deeper sequencing for metastatic prostate cancer samples
Illumina HiSeq 2500
94
EGAD00001000989
Validation/deeper sequencing for metastatic prostate cancer samples
Illumina HiSeq 2500
26
EGAD00001000990
mRNA-Seq on total RNA from primary osteoblastomas and phosphaturic mesenchymal tumours, focussing on fusion transcript expression
Illumina HiSeq 2000
11
EGAD00001000992
HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving events caused by differential SIX1 binding of the SIX1 Q177R mutatns
Illumina HiSeq 2500
3
EGAD00001000993
HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving gene expression events
Illumina HiSeq 2000
40
EGAD00001000994
HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving chromosomal aberrations
Illumina HiSeq 2000
Illumina HiSeq 2500
56
EGAD00001000995
HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving DNA alterations
Illumina HiSeq 2000
112
EGAD00001000996
Whole exome sequencing data for AML and matched normal samples
Illumina HiSeq 2500
16
EGAD00001000997
Whole-exome sequencing of a chronic lymphocytic leukemia (CLL) developed during vemurafenib treatment of a patient with malignant melanoma. Peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. DNA was extracted from highly purified (>97%) CD19+CD5+ cells obtained from the patient while being under BRAF inhibition versus CD14+ germline control cells (>90% purity). No alterations that could be linked to aberrant RAS activity or paradoxical RAF/MEK/ERK signaling could be identified in the CLL, which shows characteristic copy number alterations.
Illumina HiSeq 2500
2
EGAD00001000998
Targeted capture of exonic and intronic regions of interest for the study of genomic alterations in multiple myeloma.
Illumina HiSeq 2000
24
EGAD00001001000
Background: The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behaviour and can thereby complement the prognostically favorable 1p/19q co-deletion. Results: Genome-wide, 50 base pair single-end, sequencing was performed to detect CNAs in a clinically well-characterized cohort of 98 formalin-fixed paraffin-embedded low-grade gliomas. CNAs are correlated with overall survival as an endpoint. Seventy-five additional samples from spatially distinct regions and paired recurrent tumors of the discovery cohort were analysed to interrogate the intratumoral heterogeneity and spatial evolution. Loss of 10q25.2-qter is a frequent subclonal event and significantly correlates with an unfavorable prognosis. A significant correlation is furthermore observed in a validation set of 126 and confirmation set of 184 patients. Loss of 10q25.2-qter arises in a longitudinal manner in paired recurrent tumor specimens, whereas the prognostically favorable 1p/ 19q co-deletion is the only CNA that is stable across spatial regions and recurrent tumors. Conclusions: CNAs in low-grade gliomas display extensive intratumoral heterogeneity. Distal loss of 10q is a late onset event and a marker for reduced overall survival in low-grade glioma patients. Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor.
Illumina HiSeq 2000
175
EGAD00001001001
2
EGAD00001001002
Exome sequencing data for 8 pairs of seminomas and matched normal
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
16
EGAD00001001003
Exome sequencing of lymphocyte DNA from 12 affected individuals from six unrelated, non-syndromic Wilms tumor families.
Illumina HiSeq 2000
12
EGAD00001001004
65 prostate cancer cases wgs sequencing
Illumina HiSeq 2000
130
EGAD00001001006
Dataset for whole exome sequencing of 113 pairs of tumor and normal DNA samples along with 8 cell lines.
Illumina HiSeq 2000
234
EGAD00001001007
Low depth (4x) Illumina HiSeq raw sequence data for 100 unrelated Zulu from Durban area, South Africa.
Illumina HiSeq 2000
100
EGAD00001001008
Low depth (4x) Illumina HiSeq raw sequence data for 100 unrelated Baganda from rural Uganda.
Illumina HiSeq 2000
100
EGAD00001001009
Exome sequencing of peripheral blood from 4 individuals of a family with familial colorectal cancer type X
Illumina HiSeq 2000
4
EGAD00001001010
Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2
Ion Torrent Proton
8
EGAD00001001011
Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. Transcriptomes (RNA-Seq) and epigenomes (ChIP-Seq H3K4me1,H3K4me3,H3K27ac) in four primary cell types: monocytes, in vitro differentiated naive, tolerized and trained macrophages were characterized. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and pathways functionally implicated in trained immunity were identified. Strikingly, B-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in DNase I hypersensitive sites at cell-type specific epigenetic loci unveiled differentiation and treatment specific repertoires. Altogether, this study provides a resource to understand the epigenetic changes that underlie innate immunity in humans.
Illumina HiSeq 2000
NextSeq 500
57
EGAD00001001012
The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.
AB 5500xl Genetic Analyzer
267
EGAD00001001013
RNAseq and exome sequencing data of gastric cancer cell lines.
Illumina HiSeq 2000
30
EGAD00001001014
Illumina HiSeq 2000
2597
EGAD00001001015
Illumina HiSeq 2000
76
EGAD00001001016
DATA FILES FOR SJPhLike-RNASeq
Illumina HiSeq 2000
125
EGAD00001001017
DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.
Illumina HiSeq 2000
31
EGAD00001001018
The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations.
This dataset contains all the data available for this study on 2014-09-24
Illumina HiSeq 2000
374
EGAD00001001019
RNA-seq dataset used for the validation of CDK6 cis-regulatory mutation annotated by OncoCis. NB bam files for manuscript A_Proteomic_Chronology_of_Gene_Expression_through_the_Cell_Cycle_in_Human_Myeloid_Leukemia_Cells are now available at the following link:http://www.ebi.ac.uk/ena/data/view/ERP008483
Illumina HiSeq 2000
1
EGAD00001001020
DATA FILES FOR SJEWS-WGS
Illumina HiSeq 2000
38
EGAD00001001021
Exome sequencing of 1000 samples from the UK 1958 Birth Cohort. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.
Illumina HiSeq 2500
1000
EGAD00001001022
nccRCC RNA-Seq data of consented samples
Illumina HiSeq 2500
139
EGAD00001001023
nccRCC Whole Exome sequencing data (consented samples only)
Illumina HiSeq 2500
137
EGAD00001001024
Fastq files of 52 samples of hepatocellular carcinoma(RCAST, THCC)
Illumina HiSeq 2000
104
EGAD00001001025
The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 50-80%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.
Illumina HiSeq 2000
1156
EGAD00001001026
The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples from Birmingham will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples.
Illumina HiSeq 2000
452
EGAD00001001027
The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples.
Illumina HiSeq 2000
130
EGAD00001001028
DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.
Illumina MiSeq
18
EGAD00001001029
The dataset regards the sequencing of coding and putative regulatory sequences of 38 genes associated to either sporadic or Mendelian form of Parkinson's disease
Illumina HiSeq 2000
394
EGAD00001001031
These are only the whole exome sequences
Illumina HiSeq 2500
6
EGAD00001001032
DATA FILES FOR SJMEL-WGS
Illumina HiSeq 2000
12
EGAD00001001033
Whole exome sequencing (WES) was performed on genomic DNA derived from two patients with Sotos Syndrome Features. Sequencing (100 base pair paired-end) was performed on an Illumina Hiseq 2000 sequencer after enrichment of 62Mb of exonic and adjacent intronic sequences with TruSeq Exome Enrichment Kit (Illumina, San Diego, CA, USA).
Illumina HiSeq 2000
2
EGAD00001001034
Whole genome data (Complete genomics platform) for the study EGAS00001000824
24
EGAD00001001035
RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
66
EGAD00001001036
Illumina HiSeq 2000
26
EGAD00001001037
A total of 395 couples were subjected to IVF-PGD treatment, including 129 couples with NGS-based test and 266 couples with SNP array based test for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole genome sequencing with HiSeq 2000 platform. And the SNP array test was using Affymetrix Gene Chip Mapping Nsp I 262K. The average age of patients was 32.1 years (age range 20-44 years).
Illumina HiSeq 2000
188
EGAD00001001038
We mapped the data to the UCSC human reference genome build 37 using BWA 0.5.9-r16. We first mapped each read pair separately using bwa aln. Then we used bwa sampe to map the paired reads together to a BAM9 file. The BAM file was then sorted by genomic position and indexed using PicardTools-1.32 SortSam. To prevent PCR artifacts from influencing the downstream analysis of our data, we used Picard to mark the duplicate reads, which were ignored in downstream analysis. We used GATK IndelRealigner on our data around known indels (from 1KG Pilot). The IndelRealigner creates all possible read alignments using the source and computes the likelihood of the data containing the indel based on the read pileup. Whenever the maximum likelihood contains an indel, the reads are realigned accordingly. Each base is associated with a phred-scaled base quality score. Calibration of Phred scores is crucial as they are used in some of the downstream analysis models. We used GATK to recalibrate the base qualities with respect to (i) the base cycle, (ii) original quality score, and (iii) dinucleotide context. To minimize issues stemming from mapping problems around indels, we decided to undergo a second round of indel realignment using the GATK IndelRealigner by family rather than by individual. For this second round, we considered two sources of possible indels: 1KG Phase 1 indels and indels aligned by BWA in the GoNL data.
-
EGAD00001001039
Genomic characterisation of a large series of cancer cell lines.
Illumina HiSeq 2000
1072
EGAD00001001040
This is the complete dataset (exome and genome) for the EGAS00001000974 study.
Illumina HiSeq 2500
16
EGAD00001001041
Comparison of genomic rearrangements and DNA methylation patterns between different foci of multiple synchronous (multifocal and multicentric) invasive breast cancers.
Illumina Genome Analyzer II
Illumina HiSeq 2000
305
EGAD00001001042
In this work, using exome sequencing, we identified biallelic PNLPA6 mutations in patients with childhood blindness due to severe photoreceptor death and clinical features of Leber congenital amaurosis (LCA) and, interestingly, also of the rare Oliver McFarlane Syndrome
AB SOLiD 4 System
Illumina HiSeq 2000
7
EGAD00001001043
Illumina HiSeq 2000
8
EGAD00001001044
Ion Torrent PGM
2
EGAD00001001045
DATA FILES FOR SJRB
Illumina HiSeq 2000
20
EGAD00001001046
We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting.
Illumina HiSeq 2000
33
EGAD00001001047
Targeted exome sequencing of 375 genes
Illumina HiSeq 2500
31
EGAD00001001048
Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z
Illumina HiSeq 2000
-
EGAD00001001050
We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting.
Illumina HiSeq 2000
8
EGAD00001001051
Illumina HiSeq 2000
200
EGAD00001001052
DATA FILES FOR SJTALL
Illumina HiSeq 2000
24
EGAD00001001053
DATA FILES FOR SJOS-WGS-2ndBatch
Illumina HiSeq 2000
27
EGAD00001001054
DATA FILES FOR Ph-likeALL WES
Illumina HiSeq 2000
23
EGAD00001001055
Bam files for the whole exome sequencing from the study on Spatial homogeneity in pediatric brain tumors.
Illumina HiSeq 2000
53
EGAD00001001056
Illumina HiSeq 2000
7
EGAD00001001057
RNA-seq from normal human tissues (2 x 75 bp)
Illumina HiSeq 2000
3
EGAD00001001058
Cancer exome reads consisting of FASTQ paired end reads from bone marrow samples
Illumina HiSeq 2000
42
EGAD00001001059
Whole Exome Sequencing files accompanying Genetic landscape of pediatric Rhabdomyosarcoma
Illumina HiSeq 2000
56
EGAD00001001060
Illumina HiSeq 2000
112
EGAD00001001061
This experiment is to inform us of the validity of using pre-made library material to perform a bespoke pulldown experiment to validate the mutations found between the whole genome sequencing of the DNA from the same individuals cancer and normal material. This is to identify the valid and informative mutations in cancer genomes.
Illumina MiSeq
4
EGAD00001001062
Patient (who has had multiple malignancies) has previously been found to harbour a pathogenic p53 variant which is probably mosaic. This finding is based on exome sequencing performed elsewhere. In this study we will resequence the locus in question to ascertain whether the variant is indeed mosaic.
Illumina MiSeq
4
EGAD00001001063
Chondromxoid fibroma is a benign tumour of bone with unknown underlying pathogenesis. To determine pathognomic genomic event in chondromyxoid fibroma whole genome sequencing will be undertaken to reconstruct rearrangements and find underlying mutations.
Illumina HiSeq 2000
2
EGAD00001001064
Extension of angiosarcoma whole genome sequencing study
Illumina MiSeq
4
EGAD00001001065
DATA FILES FOR SJCPC-WGS
Illumina HiSeq 2000
8
EGAD00001001066
Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution
Illumina HiSeq 2000
Illumina MiSeq
188
EGAD00001001071
Samples from the "100" project that are in the ICGC PanCancer project.
Illumina HiSeq 2000
10
EGAD00001001072
(ShallowSeq CopyNumber)
Illumina MiSeq
5
EGAD00001001073
miRNA-seq Cohort of 140 Formalin Fixed Paraffin Embedded Diffuse Large B-cell Lymphoma Patient Samples
140
EGAD00001001074
miRNA-seq Cohort of 92 Fresh Frozen Diffuse Large B-cell Lymphoma Patient Samples
92
EGAD00001001075
miRNA-seq Cohort of 15 Benign Centroblasts
15
EGAD00001001076
Fastq files of 239 samples of biliary tract cancer
Illumina HiSeq 2000
239
EGAD00001001079
The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples.Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group.
This dataset contains all the data available for this study on 2014-11-20.
Illumina HiSeq 2000
2702
EGAD00001001080
MDS patients
5
EGAD00001001081
Healthy reference samples
3
EGAD00001001083
Illumina HiSeq 2000
2
EGAD00001001084
Illumina HiSeq 2000
209
EGAD00001001085
This dataset includes 2 pairs of tumour/normal whole genome sequence data as well as MEN1 gene targeted sequencing of an additional 87 specimens.
Illumina HiSeq 2500
Illumina MiSeq
91
EGAD00001001086
These analysis are the BAM files for the LCLs samples of the EUROBATS samples.
765
EGAD00001001087
RNAseq BAM files for the Skin samples of the EUROBATS project.
672
EGAD00001001088
RNAseq BAM files for the blood samples of the EUROBATS project
391
EGAD00001001089
RNAseq BAM files for the Fat samples of the EUROBATS project
685
EGAD00001001090
This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.
Illumina HiSeq 2000
166
EGAD00001001091
We established and validated a sequence capture based NGS testing approach for PKD1. The presence of six PKD1 pseudogenes and tremendous allelic heterogeneity make molecular genetic testing of PKD1 variants challenging. In the publication accompaying this dataset (An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease, Eisenberger et.al., PLoS one), we demonstrate that the applied standard mapping algorithm specifically aligns reads to the PKD1 locus and overcomes the complication of unspecific capture of pseudogenes. This dataset contains the raw PKD1 reads of all patients from the publication.
Illumina HiSeq 1500
55
EGAD00001001092
Approximately 80% of clinically clearly diagnosed patients suffering from primary ciliary dyskinesia (PCD) cannot be assigned to a specific gene defect. Despite extensive research on PCD and despite the increasing number of PCD genes and knowledge about their sites of action as e.g structural component or cytoplasmic pre-assembly factor, the biology of motile cilia and the pathomechanism leading to PCD is largely unknown. The aim of this study is to identify novel PCD related genes and processes relevant for motile cilia function.We will perform exome sequencing, aiming on the analysis of family trios. In these families, the diagnosis of PCD is secured, but the underlying gene defects has so far not been identified.
Illumina HiSeq 2000
150
EGAD00001001093
Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing
Illumina HiSeq 2000
2
EGAD00001001094
200PG : WGS Raw Sequence (fastq) : Raw WG sequence data (fastq) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672
Illumina HiSeq 2500
247
EGAD00001001095
Supporting data for ICGC PACA-CA Release 18
Illumina HiSeq 2000
Illumina HiSeq 2500
506
EGAD00001001096
Illumina HiSeq 2000
419
EGAD00001001098
DATA FILES FOR SJINF RNASeq
Illumina HiSeq 2000
63
EGAD00001001100
DCC Project Code:
SKCA-BR Skin Adenocarcinoma - BR Brazil
AB 5500 Genetic Analyzer
Illumina HiSeq 2500
200
EGAD00001001104
MMP-seq tumor samples, UDG treated (FASTQ)
Illumina MiSeq
16
EGAD00001001105
Whole-exome sequencing in 16 RMS casesWhole-transcriptome sequencing in 8 RMS cases
Illumina HiSeq 2000
38
EGAD00001001106
In the first part of this project, we will differentiate IPS cells from 5 human donors into macrophages, and extract RNA from unstimulated and LPS stimulated macrophages to perform RNA sequencing. We will also extract RNA before and after stimulation in blood- derived macrophages from 5 additional, unrelated healthy samples. In the second part of the project, RNA-seq data will be analysed to compare LPS response of these two macrophage populations. In summary, we will perform 75bp PE RNA-seq on 20 samples (10 pre and post stimulus), on the HiSeq 2500 platform. Samples will be multiplexed at 5 samples / lane, so we will require 4 flow cells in total.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
18
EGAD00001001107
MMP-seq cell lines (FASTQ)
Illumina Genome Analyzer IIx
154
EGAD00001001108
MMP-seq tumor samples (FASTQ)
Illumina Genome Analyzer IIx
218
EGAD00001001109
Illumina HiSeq 2000
46
EGAD00001001110
Illumina HiSeq 2000
46
EGAD00001001111
Illumina HiSeq 2000
46
EGAD00001001112
Illumina HiSeq 2000
46
EGAD00001001113
Illumina HiSeq 2000
46
EGAD00001001114
DDD DATAFREEZE 2013-12-18: 1133 trios - exome sequence BAM files (Ref: DDD Nature 2015)
-
EGAD00001001115
SeqControl
Illumina HiSeq 2500
54
EGAD00001001116
Whole Genome Sequencing Illumina HiSeq data from 95 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). This data is from batches 1 to 3 and is the bulk of the data used in Wedge et al, Nature Genetics 2018 (PMID: 29662167).
As of September 2020, some of the studies using these data include:
Wedge et al, Nature Genetics 2018 (PMID: 29662167)
Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)
Illumina HiSeq 2000
150
EGAD00001001118
Gastric Cancer (GC) is a highly heterogeneous disease. To identify potential clinically actionable therapeutic targets that may inform individualized treatment strategies, we performed whole-exome sequencing on 78 GCs of differing histologies and anatomic locations, as well as whole-genome sequencing on two GC cases, each with 3 primary tumours and 2 matching lymph node metastases. The data showed two distinct GC subtypes with either high-clonality (HiC) or low-clonality (LoC).
Illumina HiSeq 2000
168
EGAD00001001119
Whole Genome Bisulfite Sequencing
Illumina HiSeq 2000
Illumina HiSeq 2500
10
EGAD00001001120
Whole Genome Sequencing
Illumina HiSeq 2000
Illumina HiSeq 2500
26
EGAD00001001121
RNA Sequencing
Illumina HiSeq 2000
10
EGAD00001001122
FFPE normal panel generation for use with V3 cancer panel 0618521
Illumina HiSeq 2000
94
EGAD00001001123
Deep sequencing of two skin biopsies to study the landscape of somatic mutations in human adult tissues.
Illumina HiSeq 2000
2
EGAD00001001124
Our aim is to analyze the genome of human melanoma cell lines and short term culture from human melanoma samples in order to identify genes that confer drug resistance to clinically relevant targeted therapies. We will perform whole-exome sequencing, copy number variation analysis and methylome analysis in a collection of human melanoma cell lines and short term culture that will be then screened for drug sensitivity/resistance through a library of clinically relevant drugs and drug combinations. By the combined analysis of the genomic lesion and the drug sensitivity/resistance profile of different cell lines, we will look for genes whose mutation is associated to the sensitivity or resistance to a specific drug in different samples.
Illumina HiSeq 2000
14
EGAD00001001125
Exome sequencing of Untreated BCC samples.
Illumina HiSeq 2000
91
EGAD00001001126
340
EGAD00001001127
ChIP-Seq data for 2 effector memory CD8-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
2
EGAD00001001128
Bisulfite-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
3
EGAD00001001129
RNA-Seq data for 10 mature neutrophil sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
10
EGAD00001001130
DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
5
EGAD00001001131
Bisulfite-Seq data for 1 memory B cell sample(s). 20 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001132
RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001001133
Bisulfite-Seq data for 2 erythroblast sample(s). 35 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
2
EGAD00001001134
Bisulfite-Seq data for 1 precursor lymphocyte of B lineage sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001135
Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
2
EGAD00001001136
ChIP-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 13 run(s), 13 experiment(s), 13 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
2
EGAD00001001137
RNA-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
2
EGAD00001001138
ChIP-Seq data for 6 Acute promyelocytic leukemia sample(s). 25 run(s), 23 experiment(s), 23 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
6
EGAD00001001139
Bisulfite-Seq data for 3 inflammatory macrophage sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
3
EGAD00001001140
RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
4
EGAD00001001141
Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001142
RNA-Seq data for 1 endothelial cell of umbilical vein (resting) sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001143
Bisulfite-Seq data for 4 alternatively activated macrophage sample(s). 64 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
4
EGAD00001001144
ChIP-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
1
EGAD00001001145
RNA-Seq data for 2 CD38-negative naive B cell sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
2
EGAD00001001146
RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001001147
ChIP-Seq data for 7 CD4-positive, alpha-beta T cell sample(s). 46 run(s), 45 experiment(s), 45 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
7
EGAD00001001148
RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
8
EGAD00001001149
ChIP-Seq data for 7 mature neutrophil sample(s). 78 run(s), 60 experiment(s), 60 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
7
EGAD00001001150
Bisulfite-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001151
Bisulfite-Seq data for 1 endothelial cell of umbilical vein (proliferating) sample(s). 21 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001152
Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
2
EGAD00001001153
RNA-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001154
ChIP-Seq data for 5 CD8-positive, alpha-beta T cell sample(s). 28 run(s), 28 experiment(s), 28 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
5
EGAD00001001155
ChIP-Seq data for 5 alternatively activated macrophage sample(s). 36 run(s), 35 experiment(s), 35 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
5
EGAD00001001156
RNA-Seq data for 6 hematopoietic stem cell sample(s). 13 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
6
EGAD00001001157
Bisulfite-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 61 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
3
EGAD00001001158
ChIP-Seq data for 4 cytotoxic CD56-dim natural killer cell sample(s). 16 run(s), 16 experiment(s), 16 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
4
EGAD00001001159
RNA-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001001160
Bisulfite-Seq data for 1 plasma cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001161
DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
1
EGAD00001001162
Bisulfite-Seq data for 1 Acute myeloid leukemia sample(s). 18 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001163
RNA-Seq data for 1 effector memory CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001164
RNA-Seq data for 1 class switched memory B cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001165
RNA-Seq data for 5 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 23 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
5
EGAD00001001166
RNA-Seq data for 1 endothelial cell of umbilical vein (proliferating) sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001167
Bisulfite-Seq data for 3 Acute promyelocytic leukemia sample(s). 24 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
3
EGAD00001001168
ChIP-Seq data for 2 mature eosinophil sample(s). 12 run(s), 12 experiment(s), 12 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
2
EGAD00001001169
RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001001170
RNA-Seq data for 1 conventional dendritic cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001171
RNA-Seq data for 1 memory B cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001172
RNA-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001173
RNA-Seq data for 10 CD4-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
10
EGAD00001001174
RNA-Seq data for 1 regulatory T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001175
RNA-Seq data for 1 central memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001176
Bisulfite-Seq data for 1 class switched memory B cell sample(s). 20 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001177
RNA-Seq data for 7 erythroblast sample(s). 29 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
7
EGAD00001001178
RNA-Seq data for 1 Leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
1
EGAD00001001179
ChIP-Seq data for 10 CD14-positive, CD16-negative classical monocyte sample(s). 73 run(s), 69 experiment(s), 69 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
10
EGAD00001001180
Bisulfite-Seq data for 2 central memory CD8-positive, alpha-beta T cell sample(s). 27 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
2
EGAD00001001181
RNA-Seq data for 7 Acute promyelocytic leukemia sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
7
EGAD00001001182
ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
1
EGAD00001001183
ChIP-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
2
EGAD00001001184
RNA-Seq data for 5 common lymphoid progenitor sample(s). 20 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
5
EGAD00001001185
DNase-Hypersensitivity data for 2 monocyte sample(s). 4 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
2
EGAD00001001186
RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
3
EGAD00001001187
ChIP-Seq data for 3 Chronic lymphocytic leukemia sample(s). 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
3
EGAD00001001188
ChIP-Seq data for 7 Acute myeloid leukemia sample(s). 23 run(s), 23 experiment(s), 23 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
7
EGAD00001001189
Bisulfite-Seq data for 4 CD8-positive, alpha-beta T cell sample(s). 56 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
4
EGAD00001001190
DNase-Hypersensitivity data for 1 Acute myeloid leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
1
EGAD00001001191
RNA-Seq data for 8 monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
8
EGAD00001001192
Bisulfite-Seq data for 5 macrophage sample(s). 72 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
5
EGAD00001001193
DNase-Hypersensitivity data for 2 inflammatory macrophage sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
2
EGAD00001001194
ChIP-Seq data for 2 erythroblast sample(s). 14 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
2
EGAD00001001195
ChIP-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
1
EGAD00001001196
ChIP-Seq data for 13 macrophage sample(s). 55 run(s), 55 experiment(s), 55 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
NextSeq 500
13
EGAD00001001197
ChIP-Seq data for 2 monocyte sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
NextSeq 500
2
EGAD00001001198
DNase-Hypersensitivity data for 14 macrophage sample(s). 18 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811
Illumina HiSeq 2000
14
EGAD00001001199
RNA-Seq data for 18 macrophage sample(s). 19 run(s), 18 experiment(s), 18 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
18
EGAD00001001200
Bisulfite-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001201
Bisulfite-Seq data for 6 mature neutrophil sample(s). 79 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
6
EGAD00001001202
RNA-Seq data for 4 alternatively activated macrophage sample(s). 6 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811
Illumina HiSeq 2000
4
EGAD00001001203
Bisulfite-Seq data for 1 germinal center B cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
1
EGAD00001001204
ChIP-Seq data for 6 inflammatory macrophage sample(s). 35 run(s), 35 experiment(s), 35 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
6
EGAD00001001205
Bisulfite-Seq data for 3 CD38-negative naive B cell sample(s). 29 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
3
EGAD00001001206
Bisulfite-Seq data for 6 CD14-positive, CD16-negative classical monocyte sample(s). 86 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811
Illumina HiSeq 2000
6
EGAD00001001207
ChIP-Seq data for 4 CD38-negative naive B cell sample(s). 14 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811
Illumina HiSeq 2000
4
EGAD00001001208
Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient.
Illumina HiSeq 2000
Illumina HiSeq 2500
105
EGAD00001001209
To examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA, we performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. This data set contains 17 breast cancer samples that were sequenced in duplicate (n=14) or triplicate (n=3), in order to assess concordance of all calls and single nucleotide variant (SNV) calls.
AB SOLiD 4 System
37
EGAD00001001210
Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress
28
EGAD00001001212
RNAseq profile of purified plasma cells from multiple myeloma patients and tonsils of healthy donors
Illumina HiSeq 2000
15
EGAD00001001213
Illumina HiSeq 2000
5
EGAD00001001214
Deep (>25x mean coverage) whole genome sequencing on 5-10 families drawn from the Scottish Family Health Study with four or more children.
Illumina HiSeq 2000
19
EGAD00001001215
Targeted sequencing follow-up of genomic lesions in multiple myeloma.
Illumina HiSeq 2000
424
EGAD00001001216
The aim of this project is to genotype and sequence single spermatozoa from two men, one in his twenties and the other in his seventies. The resulting data is used to quantify the mutations that have arisen in the gametes of both individuals in order to better understand the effect of aging on mutation rates and modes.Project Outline. In order to quantify mutations, semen from two individuals are sequenced. 48 single sperm cells are isolated from each individual, and their DNA is extracted. The resulting genomes are amplified using PicoPlex, GenomiPhi MDA, Repli-G MDA, and MALBAC. QC step is applied to check the quality of WGA DNA using standard Sequenom plex (26 SNPs). A subset of 32 amplification products which pass the intiall QC, are genotyped using Affymetrix SNP6 chips. 12 of the genotyped amplification products are also sequenced. In addition, one multi-cell sample per individual is sequenced as a reference and for validation purposes.Altogether, 12 single cell sperm genomes and two multi-cell genomes are sequenced, coming to a total of 14 genomes. Of the single cell sperm genomes, 2 are sequenced to 50x coverage, and the other 10 to 25x coverage. Both multi-cell genomes are sequenced to 25x coverage.
Illumina HiSeq 2000
12
EGAD00001001217
15
EGAD00001001218
10
EGAD00001001220
Illumina HiSeq 1000
10
EGAD00001001221
Illumina HiSeq 2500
54
EGAD00001001222
TGCT Whole Exome Sequencing data
Illumina HiSeq 2500
84
EGAD00001001226
smRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada as part of the International Human Epigenome Consortium.
28
EGAD00001001227
Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
32
EGAD00001001228
Whole genome shotgun sequencing assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
27
EGAD00001001229
ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000;ILLUMINA
48
EGAD00001001230
ChIP-Seq (H3K27me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000;ILLUMINA
48
EGAD00001001231
ChIP-Seq (H3K36me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000;ILLUMINA
48
EGAD00001001232
ChIP-Seq (H3K4me1) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000;ILLUMINA
48
EGAD00001001233
ChIP-Seq (H3K4me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000;ILLUMINA
48
EGAD00001001234
ChIP-Seq (H3K9me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000;ILLUMINA
48
EGAD00001001235
ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
48
EGAD00001001236
Targetted capture and resequencing of 94 known myeloid genes across MPN trials (PT1 and Voriconazole study) and other MPN samples.
Illumina HiSeq 2000
1860
EGAD00001001237
This is a pilot project to determine whether the TAPG FFPE DNA's are suitable for deep sequencing. If successful an investigation of SNP distribution in a larger cohort will follow.
Illumina HiSeq 2000
15
EGAD00001001238
Extension analysis to pursue candidate genes of interest in chordoma
Illumina HiSeq 2000
262
EGAD00001001239
Extension analysis to pursue candidate genes of interest in chordoma
Illumina HiSeq 2000
262
EGAD00001001240
VCF files of somatic variants from tumor-normal pairs of Asian lung cancer patients
30
EGAD00001001242
Pilot study to set up sequencing protocols for targeted pulldown methylation profiling
Illumina MiSeq
2
EGAD00001001243
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.
Illumina HiSeq 2000
9
EGAD00001001244
RNA-sequencing (RNA-seq) was performed with RNA extracted from fresh-frozen
human tumor tissue samples. cDNA libraries were prepared from poly-A selected
RNA applying the Illumina TruSeq protocol for mRNA. The libraries were then
sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x
of the annotated transcriptome.
Illumina HiSeq 2000
59
EGAD00001001245
DATA FILES FOR PCGP SJINF WES
Illumina HiSeq 2000
40
EGAD00001001246
DATA FILES FOR PCGP SJMEL WXS
Illumina HiSeq 2000
28
EGAD00001001247
DATA FILES FOR PCGP SJMEL RNASEQ
Illumina HiSeq 2000
7
EGAD00001001248
DATA FILES FOR PCGP SJETP WXS
Illumina HiSeq 2000
13
EGAD00001001249
WES of HCC by HiSeq 2000,total 71 samples including Hepatocellular carcinoma cell lines and nornal sample(Peripheral Blood or the adjacent tissues of cancer)
Illumina HiSeq 2000
71
EGAD00001001250
Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of 8028 samples from persons of 30 years or older, which were screened for psychotic and bipolar disorders using the Composite International Diagnostic Interview, self-reported diagnoses, medical examination, and national registers.
Illumina HiSeq 2000
731
EGAD00001001251
Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of approximately 30,300 samples and comprises 500 individuals of each gender in the extreme tail of high density lipoprotein (HDL) concentrations. Included individuals were between 25 and 65 years of age. Individuals with a diagnosis of diabetes or BMI>30 were excluded from the study.
Illumina HiSeq 2000
966
EGAD00001001252
DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control.For WE sequencing we user Hybrid capture (Nimblegen version 3.0) of the lymph node and lung metastases, primary tumour and spleen normal; we generated ~100-fold coverage.
4
EGAD00001001253
DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control.WG sequencing produced ~30-fold (primary tumour, spleen normal)-50-fold (lung metastasis) coverage
3
EGAD00001001256
Clonal hematopoiesis was investigated in patients with aplastic anemia using next-generation sequencing and single-nucleotide polymorphism (SNP) array-based karyotyping.
Illumina HiSeq 2000
186
EGAD00001001257
Illumina HiSeq 2000
3
EGAD00001001258
Illumina HiSeq 2000
5
EGAD00001001259
Illumina HiSeq 2000
2
EGAD00001001260
Illumina HiSeq 2000
2
EGAD00001001261
Bisulfite-Seq of CD14-positive, CD16-negative classical monocyte samples for methylome saturation and COMET analysis
Illumina HiSeq 2000
2
EGAD00001001262
Unaligned bam of 31 samples derived from primary tumor
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
31
EGAD00001001263
Unaligned bam of 31 samples derived from blood
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
31
EGAD00001001264
We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
223
EGAD00001001265
Genomic architecture of mesothelioma parent study is project 925. This project is set up in parallel to project 925 in order to Whole genome sequence ten of the 59 tumours in that project.
HiSeq X Ten
18
EGAD00001001266
Whole genome sequencing of primary angiosarcoma
HiSeq X Ten
12
EGAD00001001267
Anaplastic meningiomas are a rare, malignant variant of meningioma. At present there is no effective treatment for this cancer. The aim of the study is to identify somatic mutations in anaplastic meningiomas. We plan to sequence a set of 500 known cancer genes in 50 anaplastic meningioma and corresponding peripheral blood DNA samples. Bioinformatics will be used to analyse the results to assess the probability of these mutations being causal and so likely of critical importance for the tumour growth. Identification of these mutations will guide selection of appropriate compounds to effectively treat the disease.
HiSeq X Ten
60
EGAD00001001268
H9 human embryonic stem cells (hESCs) were cultured in feeder-free chemically-defined conditions in medium containing 10ng/ml Activin A and 12ng/ml FGF2 (Vallier L. 2011, Methods in Molecular Biology, 690: 57-66). Chromatin immunoprecipitation was performed as described in Brown S. et al. 2011. Stem Cells 29: 1176-85 by using 5ug of anti-DPY30 antibody (Sigma, cat. number HPA043761). This protocol was performed in control hESCs (expressing a scrambled shRNA) and in hESCs stably expressing an shRNA against DPY30 (Sigma, clone n. TRCN0000131112).This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
4
EGAD00001001269
Exome bam files of 75 Individuals From Multiply Affected Coeliac Families
Illumina Genome Analyzer II
Illumina Genome Analyzer IIx
75
EGAD00001001271
Around 50 samples of pre-invasive lung cancer lesions showing subsequent clinical and pathological progression or regression
HiSeq X Ten
50
EGAD00001001272
Illumina HiSeq 2000
15
EGAD00001001273
Whole genome sequencing was performed with DNA extracted from fresh-frozen
tumor and normal material. Short insert DNA libraries were prepared with the TruSeq
DNA PCRfree sample preparation kit (Illumina) for paired-end sequencing at a
minimum read length of 2x100bp. Human DNA libraries were sequenced to an
average coverage of minimum 30x for both tumor and matched normal. Murine DNA
libraries of tumor and matched normal were both sequenced to a coverage of 25x.
Illumina HiSeq 2000
100
EGAD00001001274
Brain samples for this dataset were provided by the Medical Research Council Sudden Death Brain and Tissue Bank (Edinburgh, UK). All four individuals sampled were of European descent, neurologically normal during life and confirmed to be neuropathologically normal by a consultant neuropathologist using histology performed on sections prepared from paraffin-embedded tissue blocks. Twelve regions of the central nervous system were sampled from each individual. The regions studied were: cerebellar cortex, frontal cortex, temporal cortex, occipital cortex, hippocampus, the inferior olivary nucleus (sub-dissected from the medulla), putamen, substantia nigra, thalamus, hypothalamus, intralobular white matter and cervical spinal cord.
Illumina HiSeq 2000
48
EGAD00001001275
Illumina HiSeq 2000
1
EGAD00001001276
McGill EMC Release 4 for cell type "induced pluripotent stem cell"
unspecified
8
EGAD00001001277
McGill EMC Release 4 in tissue "fat pad" for cell type "fat cell"
unspecified
1
EGAD00001001278
McGill EMC Release 4 in tissue "venous blood" for cell type "B cell"
unspecified
41
EGAD00001001279
McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive helper T cell"
unspecified
55
EGAD00001001280
McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive, alpha-beta T cell"
unspecified
40
EGAD00001001281
McGill EMC Release 4 in tissue "venous blood" for cell type "eosinophil"
unspecified
3
EGAD00001001282
McGill EMC Release 4 in tissue "venous blood" for cell type "Monocyte"
unspecified
82
EGAD00001001283
McGill EMC Release 4 in tissue "venous blood" for cell type "T cell"
unspecified
20
EGAD00001001284
McGill EMC Release 4 in tissue "Brodmann (1909) area 11"
unspecified
1
EGAD00001001285
McGill EMC Release 4 in tissue "Brodmann (1909) area 44"
unspecified
1
EGAD00001001286
McGill EMC Release 4 in tissue "Brodmann (1909) area 8;Brodmann (1909) area 9"
unspecified
1
EGAD00001001287
McGill EMC Release 4 in tissue "kidney"
unspecified
2
EGAD00001001288
McGill EMC Release 4 in tissue "skeletal muscle tissue"
unspecified
29
EGAD00001001289
McGill EMC Release 4 for assay "Bisulfite-seq": Methylation profiling by high-throughput sequencing
unspecified
44
EGAD00001001290
McGill EMC Release 4 for assay "RNA-seq": Transcriptome profiling by high-throughput sequencing
unspecified
261
EGAD00001001291
McGill EMC Release 4 for assay "mRNA-seq": Transcriptome profiling by high-throughput sequencing
unspecified
40
EGAD00001001292
McGill EMC Release 4 for assay "smRNA-seq": Transcriptome profiling by high-throughput sequencing
unspecified
6
EGAD00001001293
McGill EMC Release 4 for assay "ChIP-Seq Input"
unspecified
52
EGAD00001001294
McGill EMC Release 4 for assay "H3K27me3"
unspecified
32
EGAD00001001295
McGill EMC Release 4 for assay "H3K36me3"
unspecified
37
EGAD00001001296
McGill EMC Release 4 for assay "H3K4me1"
unspecified
41
EGAD00001001297
McGill EMC Release 4 for assay "H3K4me3"
unspecified
42
EGAD00001001298
McGill EMC Release 4 for assay "H3K27ac"
unspecified
36
EGAD00001001299
McGill EMC Release 4 for assay "H3K9me3"
unspecified
29
EGAD00001001300
McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688)
unspecified
1
EGAD00001001301
Whole exome sequencing data of 5 patients diagnosed with FL that had undergone several relapse episodes without evidence of transformation
Illumina HiSeq 2500
29
EGAD00001001302
Illumina HiSeq 2500
2
EGAD00001001303
The dataset for the PROP1 study consists of samples of patients with combined pituitary hormone deficiency due to two most prevalent mutations in the PROP1 gene (c.301_302delGA and c.150delA) and healthy relatives and controls. All subjects were genotyped for 21 single nucleotide polymorphisms surrounding the PROP1 gene in order to assess the potential ancestral origin of the respective mutations. The genotype data are displayed in the vcf format.
328
EGAD00001001304
We used whole-genome bisulfite sequencing (WGBS) to generate unbiased DNA methylation maps of six purified B-cell subpopulations: hematopoietic progenitor cells (HPC); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); germinal center B cells (gcBC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). WGBS was performed in 2 biological replicates from each subpopulation.
Illumina HiSeq 2000
10
EGAD00001001305
Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor
9
EGAD00001001306
Human melanoma samples were collected pre, on, and progression on BRAF inhibitor therapy. RNA was extracted and run on RNA-seq. This has provided insights into different categories of BRAF inhibitor resistance mechanisms.
Illumina HiSeq 2000
38
EGAD00001001307
Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001308
Genome and transcriptome sequence data from a primary unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
MinION
PromethION
3
EGAD00001001309
Genome and transcriptome sequence data from an appendix cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001310
Genome and transcriptome sequence data from a peritoneal mesothelioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
2
EGAD00001001311
Genome and transcriptome sequence data from a peritoneal mesothelioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001312
Fastq data for whole genome bisulfite sequencing assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
30
EGAD00001001313
We enriched a panel of cancer associated genes using the Custom Sure Select Target Enrichment Kit. Identified mutations were validated with deep sequencing in order to assess mutated allele frequencies more accurately.
Illumina MiSeq
10
EGAD00001001314
Sequence data from L1-amplicon libraries prepared from plasma-DNA from a set of 24 female controls and 18 male controls without malignant disease and samples from patients breast (n= 28) and prostate cancer patients (n=61).
Illumina MiSeq
125
EGAD00001001315
Phenotype determination by SNP-Typing using PCR and snapshotPCR with subsequent fragment analysis. We investigated 400 individuals from Northern Germany and detected up to 12 different SNPs to determine eye, hair and skin colour. More than 1000 different runs on a ABI3130 were performedThis dataset includes:- Phenotype information for 400 samples- Summary and complete genotype calls for 12 SNPs on 400 samples.
399
EGAD00001001316
Exome sequence analysis of individuals with severe early onset inflammatory bowel disease, and their families. Individuals are ascertained through the COLORS in IBD study, which includes centres throughout UK and Europe.
Illumina HiSeq 2000
Illumina HiSeq 2500
149
EGAD00001001317
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
12
EGAD00001001319
The aim of this study is to ascertain whether leukaemic mutations exist within the blood of people with otherwise normal haematopoeisis. To satisfy this aim we plan to look for 7 known leukaemic mutations in the whole blood DNA of a large cohort of blood donors who have normal haematopoesis. Genomic regions around mutational sites have been amplified using a 2 step PCR process which involves barcoding of individual patients
Illumina MiSeq
5817
EGAD00001001320
This is a study to test ATAC-seq protocols. CD4+ and CD8+ cells have been obtained from three different anatomical compartments. We aim to assay open-chromatin regions across these cells and perform comparative analyses.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
Illumina MiSeq
138
EGAD00001001321
This dataset includes WGS & WTS alignment data generated from 1 ATC tumor, its matched peripheral blood specimen and 3 authenticated ATC cell lines, THJ-16T, THJ-21T and THJ-29T. In addition, it includes WTS data from extra 4 unique anaplastic cell lines, ACT-1, C643, HTh7 and T238.
Illumina HiSeq 2000
Illumina HiSeq 2500
13
EGAD00001001322
A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing.
Illumina HiSeq 2000
196
EGAD00001001326
Whole genome sequencing of single adult t-cell leukemia/lymphoma case
Illumina HiSeq 2000
2
EGAD00001001329
Aligned Sequence (bam format), Duplicates removed
28
EGAD00001001330
In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies.
Illumina HiSeq 2000
70
EGAD00001001331
The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.
Illumina HiSeq 2000
24
EGAD00001001332
Development of a method for separation and parallel sequencing of the genomes and transcriptomes of single cells.
HiSeq X Ten
Illumina HiSeq 2500
Illumina MiSeq
700
EGAD00001001333
Whole exome sequencing BAM files for samples from the BRIDGE Consortium with pathogenic or likely pathogenic variants on genes linked to bleeding or platelet disorders.
Illumina HiSeq 2000
28
EGAD00001001334
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
99
EGAD00001001335
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina Genome Analyzer II
Illumina HiSeq 2000
28
EGAD00001001336
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
6
EGAD00001001337
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
Illumina HiSeq 2500
Illumina MiSeq
607
EGAD00001001338
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina Genome Analyzer II
Illumina HiSeq 2000
49
EGAD00001001339
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
76
EGAD00001001340
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
20
EGAD00001001341
We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Illumina HiSeq 2000
158
EGAD00001001343
Data from the study of subclonal metastatic expansion in prostate cancer. Whole genome shotgun sequencing of fifteen samples, tumour and whole blood, from the four initial patients.
Illumina HiSeq 2000
15
EGAD00001001344
Data from the study of subclonal metastatic expansion in prostate cancer. Whole genome shotgun sequencing of six samples, tumour and whole blood, from the three additional patients whose somatic variants were examined in depth.
Illumina HiSeq 2000
6
EGAD00001001345
Data from the study of subclonal metastatic expansion in prostate cancer. RNA-seq of twelve samples, tumour and benign tissue, from the four initial patients.
Illumina HiSeq 2000
12
EGAD00001001347
Exome sequencing of a case of lethal EBV-driven LPD
Illumina HiSeq 2000
3
EGAD00001001349
Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
Illumina HiSeq 2000
4
EGAD00001001350
Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
Illumina HiSeq 2000
8
EGAD00001001351
Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
Illumina HiSeq 2000
2
EGAD00001001352
Data files for CONSERTING (WGS)
Illumina HiSeq 2000
38
EGAD00001001353
Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
Illumina HiSeq 2000
2
EGAD00001001354
Whole exome sequencing of around 700 inflammatory bowel disease cases.This data can only be used for the identification of IBD/immune-mediated disease loci.
Illumina HiSeq 2000
702
EGAD00001001355
DDD DATAFREEZE 2013-12-18: 1133 trios - VCF files (Ref: DDD Nature 2015)
-
EGAD00001001356
Neuroblastoma, a clinically heterogeneous pediatric cancer, is characterized by distinct genomic profiles but few recurrent mutations. As neuroblastoma is expected to have high degree of genetic heterogeneity, study of neuroblastoma's clonal evolution with deep coverage whole-genome sequencing of diagnosis and relapse samples will lead to a better understanding of the molecular events associated with relapse. Samples were included in this study if sufficient DNA from constitutional, diagnosis and relapse tumors was available for WGS. Whole genome sequencing was performed on trios (constitutional, diagnose and relapse DNA) from eight patients using Illumina Hi-seq2500 leading to paired-ends (PE) 90x90 for 6 of them and 100x100 for two. Expected coverage for sample NB0175 100x100bp was 30X for tumor and constitutional samples. For the seven other patients expected coverage was 80X for tumor samples with PE 100x100, 100X in the other tumor samples and 50X for all constitutional samples (see table 1). Following alignment with BWA (Li et al., Oxford J, 2009 Jul) allowing up to 4% of mismatches, bam files were cleaned up according to the Genome Analysis Toolkit (GATK) recommendations (Van der Auwera et al., Current Protocols in Bioinformatics, 2013, picard-1.45, GenomeAnalysisTK-2.2-16). Variant calling was performed in parallel using 3 variant callers: GenomeAnalysisTK-2.2-16, Samtools-0.1.18 and MuTect-1.1.4 (McKenna et al., Genome Res, 2010; Li et al., Oxford J, 2009 Aug; Cibulskis et al., Nature, 2013). Annovar-v2012-10-23 with cosmic-v64 and dbsnp-v137 were used for the annotation and RefSeq for the structural annotation. For GATK and Samtools, single nucleotide variants (SNVs) with a quality under 30, a depth of coverage under 6 or with less than 2 reads supporting the variant were filter out. MuTect with parameters following GATK and Samtools thresholds have been used to filter our irrelevant variants. .SNVs within and around exons of coding genes overlapping splice sites.. Then,variants reported in more than 1% of the population in the 1000 genomes (1000gAprl_2012) or Exome Sequencing Project (ESP6500) have been discarded in order to filter polymorphisms. Finally, synonymous variants were filtered out. MuTect focuses on somatic by filtering with constitutional sample. Mpileup comparison between constitutional and somatic DNAs allowed us to focus also on tumor specific SNVs with GATK and Samtools. Finally, every SNV called by our pipeline and also supported in any constitutional samples were filtered our in order to prevent putative constitutional DNA coverage deficiency. Then we analyzed CNVs (copy number variants) with HMMcopy-v0.1.1 (Gavin et al., Genome Res, 2012) and control-FREEC-v6.7 (Boeva et al., Bioinformatics 2011) with a respective window of 2000bp and 1000 bp, and auto-correction of normal contamination of tumor samples for Control-FREEC. Finally we explored Structural variants (SVs) including deletions, inversions, tandem duplications and translocations using DELLY-v0.5.5 with standard parameters (Rausch et al., Oxford J, 2012). In tumors, at least 10 supporting reads were required to make a call and 5 supporting reads for the sample NB0175 with a coverage of only 40X (see table 2). To predict SVs in constitutional samples for subsequent somatic filtering, only 2 supporting reads were required in order not to miss one. To identify somatic events, all the SVs in each normal sample were first flanked by 500 bp in both directions and any SVs called in a tumor sample which was in the combined flanked regions of respective normal sample was removed (see graph 1). Deletions with more than 5 genes impacted or larger than 1Mb and inversions or tandem duplications covering more than 4 genes, were removed. We focused on exonic and splicing events for deletions, inversions, and tandem duplications. For translocation, we keep all SVs that occurred in intronic, exonic, 5'UTR, upstream or splicing regions. Bioinformatics detection of variations with Deep sequencing approach Once PE reads merged and adaptors trimmed by SeqPrep with default parameters, merged reads were aligned via the BWA (Li H. and Durbin R. 2009 PMID 19451168) allowing up to 1 differences in the 22-base-long seeds and reporting only unique alignments. Only reads having a mapping quality 20 or more have been further analysed. Variant calling software was not used, since we aimed to predict variations at low frequencies, observed in less than 1% of reads. Such variants require a custom approach. Using DepthOfCoverage functions of the Genome Analysis Toolkit (GATK) v2.13.2 (McKenna A, et al., 2010 Genome Research PMID: 20644199), we focused on high quality coverage of bases A, C, G and T at the targeted variant position. Depth of coverage of each base following a mapping quality higher than 20 and a base quality higher than 10 have been taken into account in order to focus only on high quality data. Aiming to determine the background level of variability at the studied regions, 10 control samples were included in the analysis. The same approach and filtering criteria have been applied as introduced above over the entire amplicons. In order to highlight variants, for each sample the frequencies of each bases at each amplicon position were then compared to those observed in the set of controls. Statistical analyses were performed with the R statistical software (http://www.R-project.org). Fisher’s exact two-sided tests with a Bonferroni correction were performed to compare percentages of bases between the data sets, i.e. for a given base between a case and the controls. Finally, significant variations were filtered-in once (i) a significant increase in the percentage of avariant base and (ii) a significant decrease in the percentage of it's reference base following our p.values criteria was observed (p.val < 0.05).
Illumina HiSeq 2500
25
EGAD00001001357
Genomic characterisation of a large series of cancer cell lines.
Illumina HiSeq 2000
462
EGAD00001001358
463 newly diagnosed patients from the UK Myeloma XI clinical trial (NCT01554852) underwent whole exome sequencing plus targeted capture of the IGH/K/L and MYC loci. 200 ng of DNA were processed using NEBNext DNA library prepartion kit and hybridised to the SureSelect Human All Exon V5 Plus. Four samples were pooled and run on one lane of a HiSeq 2000 using 76-bp paired end reads. DNA from CD138+ selected bone marrow cells (myeloma tumour) as well as peripheral white blood cells were analysed and somatic mutations detected.
Illumina HiSeq 2000
926
EGAD00001001359
Dataset contains Exome-seq and RNA-seq from 2 GBM patients, as well as RNA-seq from the derived cultured cells (GNS).
6
EGAD00001001360
The majority of neuroblastoma patients have tumors that initially respond to chemotherapy, but a large proportion of patients will experience therapy-resistant relapses. The molecular basis of this aggressive phenotype is unknown. Whole genome sequencing of 23 paired diagnostic and relapsed neuroblastomas showed clonal evolution from the diagnostic tumor with a median of 29 somatic mutations unique to the relapse sample. Eighteen of the 23 relapse tumors (78%) showed RAS-MAPK pathway mutations. Seven events were detected only in the relapse tumor while the others showed clonal enrichment. In neuroblastoma cell lines we also detected a high frequency of activating mutations in the RAS-MAPK pathway (11/18, 61%) and these lesions predicted for sensitivity to MEK inhibition in vitro and in vivo. Our findings provide a rationale for genetic characterization of relapse neuroblastoma and show that RAS-MAPK pathway mutations may function as a biomarker for new therapeutic approaches to refractory disease.
221
EGAD00001001363
To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2500
12
EGAD00001001364
This dataset contains whole exome data from 8 esophageal adenocarcinoma tumors, that has been subjected to multiregion sequencing, ranging from 3-8 regions per tumor. In total, 40 tumor samples and 8 normal blood samples have been sequenced on Illumina HiSeq 2500 at a median dept of 90x.
Illumina HiSeq 2500
47
EGAD00001001372
All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples.
Illumina HiSeq 2000
100
EGAD00001001373
The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.
Illumina HiSeq 2000
7
EGAD00001001374
The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released.
Illumina HiSeq 2500
6
EGAD00001001375
Samples will be from the BRF113683 (BREAK-3) study which is a Phase III Randomized, Open-label Study Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma (n=250 enrolled)*NGS [Agilent capture (Sanger V2 panel): 360 genes and 20 gene fusions; Illumina HiSEQ Sequencing]*CNV: [via NGS or Affy SNP 6.0 or Illumina Omni (TBD)]Bioinformatics: Analysis will be performed using core Sanger informatics pipelines similar to those previously described (Papaemmanuil E et al. (2013) Blood. 22:3616 -3627). Briefly, copy number analysis will be performed using the ASCAT algorithm, and base substitutions, small insertions and deletions using the CAVEMAN and Pindel algorithms, respectively. Statistical approaches including generalized linear models will be used to predict clinical variables such as maximum clinical response and duration of response using genetic data. Sanger and EBI to conduct analysis; Raw data and correlation with clinical endpoints to be analyzed by both EBI/Sanger and GSK (unique pipeline analyses to increase call confidence)
Illumina HiSeq 2500
169
EGAD00001001379
Illumina HiSeq 2000
29
EGAD00001001380
All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate high-coverage sequencing data for 3 Egyptian samples.
Illumina HiSeq 2000
3
EGAD00001001381
This dataset includes 69 sampels of whole-exome sequencing data of high-grade serous ovarian carcinoma (HGSOC). We included patients with advanced (International Federation of Gynecology and bstetrics [FIGO] stage IIIeIV) HGSOC for which biopsies were obtained during debulking surgery, the first at initial diagnosis and the second at disease relapse. Where possible, matched normal DNA from each participating patient was obtained from a whole-blood sample. Written informed consent was obtained from all patients and approved by the local ethics committee.
Illumina HiSeq 2000
69
EGAD00001001382
TwinsUK whole exome sequencing using NimbleGen SeqCap EZ
248
EGAD00001001383
TwinsUK whole exome sequencing using NimbleGen 2.1M SeqCap
242
EGAD00001001384
Mutations that activate the RAF-MEK-ERK signaling pathway, in particular BRAFV600E, occur in many cancers, and mutant BRAF-selective inhibitors have clinical activity in these diseases. Activating BRAF alleles are usually considered to be mutually exclusive with mutant RAS, whereas inactivating mutations in the D594F595G596 motif of the BRAF activation segment can coexist with oncogenic RAS and cooperate via paradoxical MEK/ERK activation. We determined the functional consequences of a largely uncharacterized BRAF mutation, F595L, which was detected along with an HRASQ61R allele by clinical exome sequencing in a patient with histiocytic sarcoma and also occurs in epithelial cancers, melanoma, and neuroblastoma, and investigated its interaction with mutant RAS. We demonstrate that, unlike previously described DFG motif mutants, BRAFF595L is a gain-of-function variant with intermediate activity towards MEK that does not act paradoxically, but nevertheless cooperates with mutant RAS to promote oncogenic signaling. Of immediate clinical relevance, BRAFF595L shows divergent responses to different mutant BRAF-selective inhibitors, whereas signaling driven by BRAFF595L with and without mutant RAS is efficiently blocked by pan-RAF and MEK inhibitors. Mutation data from primary patient samples and cell lines show that BRAFF595L, as well as other BRAF mutations with intermediate activity, frequently coincide with mutant RAS in a broad spectrum of cancers. These data define a novel class of activating BRAF mutations that cooperate with oncogenic RAS in a non-paradoxical fashion to achieve an optimal level of MEK-ERK signaling, extend the spectrum of patients with systemic histiocytic disorders and other malignancies who are candidates for therapeutic blockade of the RAF-MEK-ERK pathway, and underscore the value of comprehensive genetic profiling for understanding the signaling requirements of individual cancers.
Illumina HiSeq 2500
2
EGAD00001001385
Exome sequencing in 3 Möbius patients
AB SOLiD 4 System
3
EGAD00001001386
Whole Genome Sequencing of Huh7 cell lines
Illumina HiSeq 2000
Illumina HiSeq 2500
2
EGAD00001001387
Using high-throughput sequencing technologies and analytical tools, we conduct an exome sequencing study that will help understand the population
genetics of a Croatian island isolate, in a sample of 200 subjects from the Adriatic island of Vis who were
selected to reflect islanders with at least four known ancestors in grandparental line who are original islanders.
Illumina HiSeq 2000
193
EGAD00001001388
Whole-genome bisulfite sequencing (WGBS) on 30 breast cancer cases from the BASIS project.
Illumina HiSeq 2000
30
EGAD00001001389
Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung
Illumina HiSeq 2500
15
EGAD00001001390
Human monocytes from a healthy male blood donor were obtained after written informed consent and anonymised. Library preparation was performed essentially as described in the “Whole‐genome Bisulfite Sequencing for Methylation Analysis (WGBS)” protocol as released by Illumina. The library was sequenced on an Illumina HiSeq2500 using 101 bp paired-end sequencing. Read mapping was done with BWA.
1
EGAD00001001391
Illumina HiSeq 2000
3
EGAD00001001393
The aim of this study is to assess translational changes in macrophages over a time course of Salmonella infection.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2000
52
EGAD00001001394
Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357
Illumina HiSeq 2000
-
EGAD00001001395
Background: Invasive lobular breast cancer (ILBC) is the second most common histological subtype after ductal breast cancer (IDBC). In spite of significant clinical and pathological differences, ILBC is still treated as IDBC. Here, we aimed at identifying recurrent genomic alterations in ILBC with potential clinical implications.Methods: Starting from 630 ILBC primary tumors with a median follow up of 10 years, we interrogated oncogenic substitutions and indels of 360 cancer genes and genome-wide copy number alterations in 413 and 170 ILBC samples, respectively, and correlated those findings with clinical, pathological, and outcome features. The Cancer Genome Atlas database was used for comparison of frequency estimates.Results: Besides the high mutation frequency of CDH1 in 65% of the tumors, alterations in one of the three key genes of the PI3K pathway, PIK3CA, PTEN and AKT1, were present in more than half of the cases. ERBB2 and ERBB3 were mutated in 5.1 and 3.6% of the tumors. FOXA1 mutations and ESR1 copy number gains were detected in 9% and 25% of the samples. All these alterations were more frequent in ILBC than IDBC. The histological diversity of ILBC was associated with specific genomic alterations, such as enrichment for ERBB2 mutations in the mixed, non-classic subtype, and for ARID1A mutations and ESR1 gains in the solid subtype. Finally, ERBB2 and AKT1 mutations were associated with short-term risk of relapse, and chromosome 1q and 11p gain with increased and decreased breast cancer free survival, respectively.Conclusion: ERBB2, ERBB3 and AKT1 mutations represent high prevalence therapeutic targets in ILBC. FOXA1 mutations and ESR1 gains urgently deserve dedicated clinical investigation, especially in the context of endocrine treatment.
Illumina HiSeq 2000
541
EGAD00001001397
We sequenced 292 patients who were suffering NSCLC with Whole genome sequencing or Exome sequencing method.
Illumina HiSeq 2000
72
EGAD00001001398
We sequenced 205 patients who were suffering NSCLC with Exome sequencing method.
Illumina HiSeq 2000
147
EGAD00001001399
Data represent genome-wide DNA methylation profiles obtained by MethylCap-seq (Diagenode’s MethylCap-kit based purification followed by Illumina GAIIx sequencing), for 70 brain tissue samples, including 65 glioblastoma samples and 5 non-tumoral tissues (obtained from epilepsy surgery).
Illumina Genome Analyzer IIx
70
EGAD00001001400
Fastq data for whole genome shotgun sequencing assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
27
EGAD00001001401
Fastq data for smRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
28
EGAD00001001402
Fastq data for stranded mRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
32
EGAD00001001403
Fastq data for ChIP-Seq (H3K27ac) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
48
EGAD00001001404
Fastq data for ChIP-Seq (H3K27me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
48
EGAD00001001405
Fastq data for ChIP-Seq (H3K36me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
48
EGAD00001001406
Fastq data for ChIP-Seq (H3K4me1) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
48
EGAD00001001407
Fastq data for ChIP-Seq (H3K4me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
48
EGAD00001001408
Fastq data for ChIP-Seq (H3K9me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
48
EGAD00001001409
Fastq data for ChIP-Seq (Input) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2000
Illumina HiSeq 2500
48
EGAD00001001410
Whole-exome sequencing of 81 tumor/normal pairs of adult T-cell leukemia/lymphoma
Illumina HiSeq 2000
162
EGAD00001001411
RNA sequencing of 57 tumor samples of adult T-cell leukemia/lymphoma as well as 3 samples of HTLV-1 carrier and 3 samples of healthy volunteers.
Illumina HiSeq 2000
63
EGAD00001001412
Whole genome sequencing of 48 tumor/normal pairs obtained from adult T-cell leukemia/lymphoma. This data set includes 11 full-pass WGS and 37 low-pass WGS data.
HiSeq X Ten
Illumina HiSeq 2000
96
EGAD00001001413
DDD DATAFREEZE 2013-12-18: 1133 trios - README, family trios, phenotypes, validated DNMs (Ref: DDD Nature 2015)
-
EGAD00001001415
DATA FILES FOR PCGP Dyer_iPSC WGS
Illumina HiSeq 2000
2
EGAD00001001416
DATA FILES FOR PCGP Dyer_iPSC TEBS
Illumina HiSeq 2000
18
EGAD00001001417
bam files associated with the study EGAS00001001205
6
EGAD00001001418
DATA FILES FOR PCGP Dyer_iPSC 5hmc
Illumina HiSeq 2000
8
EGAD00001001421
Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients
Illumina MiSeq
125
EGAD00001001422
HipSci - Bardet-Biedl Syndrome - Exome Sequencing - April 2015
Illumina HiSeq 2000
3
EGAD00001001423
Illumina HiSeq 2000
7
EGAD00001001424
We obtained paired longitudinal specimens from a total of 38 glioblastoma (GBM) patients (34 primary and 4 secondary GBM patients). Treatment-naive initial tumors were available for 35 cases; for the other 3 cases, we used the first available recurrent tumors in lieu of initial tumors. Tumor specimens were subjected to whole-exome sequencing (27 of 38 cases, with the matched normal/blood for 22 of the 27 cases) and transcriptome sequencing (30 of 38 cases).
Illumina HiSeq 2000
Illumina HiSeq 2500
141
EGAD00001001425
The objectives of this project are the identification of markers related to cancer therapy resistance in the blood of breast cancer patients and to study the genetic changes in cancer cells during this development of resistance. Whole genome amplified DNA from Circulating Tumor Cells (CTCs), selected during the course of systemic treatment from blood of metastatic breast cancer patients, will be exome sequenced . The patients selected for this study did not respond to therapy.
Illumina HiSeq 2000
149
EGAD00001001426
Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression.
We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity.
This dataset contains all the data available for this study on 2015-07-02.
Illumina HiSeq 2000
446
EGAD00001001427
Targeted cancer gene sequencing of samples enrolled in the SSGXVIII trial from Finland.
Illumina HiSeq 2000
312
EGAD00001001428
Identification of human deubiquitylating enzymes whose knock out result in hypersensitivity to DNA damaging agents, by comparing the sequence reads of 'barcode region' from mixed cell culture.
Illumina HiSeq 2000
6
EGAD00001001429
Profiling subclonal architecture and phylogeny in tumors by whole-genome sequence data mining and single-cell genome sequencing
HiSeq X Ten
2
EGAD00001001430
Investigation into causal genes underlying anaplastic meningioma
Illumina HiSeq 2000
73
EGAD00001001431
SCLC - RNA sequencing data Publication Peifer et al., 2012, Nature Genetics
Illumina HiSeq 2000
15
EGAD00001001432
PCGP Germline Study Whole Genome Sequencing
Illumina HiSeq 2000
1337
EGAD00001001433
PCGP Germline Study Whole Exome Sequencing
Illumina HiSeq 2000
906
EGAD00001001435
Aligned whole genome bisulfite sequencing data for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
30
EGAD00001001436
AB 5500 Genetic Analyzer
4
EGAD00001001437
HipSci - Healthy Normals - Exome Sequencing - April 2015
Illumina HiSeq 2000
122
EGAD00001001438
HipSci - Healthy Normals - RNA Sequencing - May 2015
Illumina HiSeq 2000
116
EGAD00001001439
Mammary cell samples from donors 28/32/33. Contains 12 MiSeq sequencefiles and 12 alignment files derived from HiSeq runs.
Illumina MiSeq
12
EGAD00001001440
This project entailed generation of high depth WGS (30x) of 100 individuals from the general Greek population.
HiSeq X Ten
100
EGAD00001001441
Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long non-coding RNAs (lncRNAs), on the way MYC is able to influence cellular transcriptome. To this aim we have intersected RNA-sequencing data from two MYC-inducible cell lines and from a cohort of 91 mature B-cell lymphomas carrying, or not carrying, genetic variants resulting in MYC over-expression. By this approach, we identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them we focused on a lncRNA that we named MINCR, for MYC-Induced long Non-Coding RNA, showing a strong correlation with MYC expression in MYC-positive lymphomas and also in pancreatic ductal adenocarcinomas. To understand its cellular role we performed RNA interference (RNAi) experiments and found that MINCR knock-down is associated with a reduction in cellular viability, due to an impairment in cell cycle progression. Differential gene expression analysis following RNAi showed a strongly significant enrichment of cell cycle genes among the genes down-regulate following MINCR knock-down. Interestingly these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of MYC transcriptional program. Accordingly, following MINCR knock-down, we observed a reduction in the binding of MYC to the promoters of selected cell cycle genes. Finally we provide evidences that down-regulation of AURKA, AURKB and CTD1 may explain the reduction in cellular proliferation observed upon MINCR knock-down. We therefore suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes.
Illumina HiSeq 2000
Illumina HiSeq 2500
49
EGAD00001001442
This project is to explore the contribution of de novo mutations to severe structural malformations diagnosed prenatally using ultrasound. These malformations include heart, CNS, renal and GI abnormalities. In this pilot project we aim to exome sequence 30 parent-foetus trios to ~50X mean coverage and identify de novo functional variants using an algorithm developed in the Hurles group
Illumina HiSeq 2000
86
EGAD00001001443
RNASeq sequencing.
Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2 × 76 bp. We generated more than 20 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina Inc.) following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files.
Illumina Genome Analyzer II
199
EGAD00001001444
Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants and young children. Although the prognosis of ATRT patients is poor, some patients respond very well to current treatments, suggesting inter-tumor molecular heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large cohort of ATRTs (n = 170). Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location and type of SMARCB1 alterations, were identified using DNA-methylation or gene expression analyses. Whole genome DNA- and RNA-sequencing found no other recurrent mutations explaining the differences between subgroups. However, whole genome bisulfite-sequencing and H3K27Ac ChIP-sequencing of primary tumors revealed clear differences in methylation patterns and enhancer landscapes, leading to the identification of subgroup-specific regulatory networks.
Illumina HiSeq 2000
Illumina HiSeq 2500
55
EGAD00001001445
Deep sequencing of melanoma for driver mutations
Illumina MiSeq
3
EGAD00001001446
Genomic and transcriptomic characterization of drug-resistant colon cancer stem cell lines.
Illumina HiSeq 2000
4
EGAD00001001447
Whole genome sequencing of single cell derived organoids from normal colon tissue and colorectal cancer.
HiSeq X Ten
73
EGAD00001001448
Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.
Illumina MiSeq
11
EGAD00001001449
PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina MiSeq
6
EGAD00001001450
This study is to ascertain whether it is feasible to extract single cell from a tumour, perform amplification, generate a library and sequence a targeted pulldown.
Illumina HiSeq 2000
3
EGAD00001001451
JMML targeted sequencing of candidate genes
Illumina MiSeq
75
EGAD00001001452
Anaplastic oligodendrogliomas (AOs) are rare primary brain tumors which are generally incurable, with heterogeneous prognosis and few treatment targets identified. Most oligodendrogliomas have chromosome 1p/19q co-deletion and IDH mutation. We analyzed 51 AOs by whole-exome sequencing, identifying previously reported frequent somatic mutations in CIC and FUBP1. We also identified recurrent mutations in TCF12 and in an additional series of 83 AO. Overall 7.5% of AO are mutated for TCF12, which encodes an oligodendrocyte-related transcription factor. 80% of TCF12 mutations identified were in either the bHLH domain, which is important for TCF12 function as a transcription factor, or were frame shift mutations leading to TCF12 truncated for this domain. We show that these mutations compromise TCF12 transcriptional activity and are associated with a more aggressive tumor type. Our analysis provides further insights into the unique and shared pathways driving AO.
Illumina HiSeq 2000
102
EGAD00001001453
The project is to evaluate the genomic binding sites of the histone demethylase JARID1C. This gene was recently identified in CGP as a novel recessive cancer gene in human renal cell carcinoma.
Illumina Genome Analyzer II
4
EGAD00001001454
Previously we performed deep WGS on 6 parents and 13 children from 3 large families from the Scottish Family Health Study to identify de novo mutations. This prelim is cover the additional sequencing of one grandchild from one of these three families. The inclusion of a third generation individual will provide additional experimental validation for the de novo mutations found in the initial trio. As in the previous study, the DNA will be WGS to a depth of approximately 25X to achieve this purpose.These data can only be used for the investigation of the genetic causes of the reported clinical phenotypes in these patients
Illumina HiSeq 2000
1
EGAD00001001456
1000Genomes imputed data set of 581 cases and 417 controls for male-pattern baldness
1
EGAD00001001457
All samples from the "100" project
Illumina HiSeq 2000
24
EGAD00001001458
Whole genome sequencing of EBV-transformed B cells in order to determine whether EBV induction of activation-induced cytidine deaminase (AID) produces genome-wide mutations and/or chromosomal rearrangements.
HiSeq X Ten
12
EGAD00001001459
Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer.
This dataset contains all the data available for this study on 2015-08-05.
Illumina HiSeq 2000
76
EGAD00001001460
Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH).
This dataset contains all the data available for this study on 2015-08-05.
Illumina HiSeq 2000
62
EGAD00001001461
CBP has opposing functions during cerebellar development and is a targetable tumor suppressor at late stages of medulloblastoma initiation
30
EGAD00001001462
Exome sequencing of 142 samples with corresponding Sanger sequencing results for 416 variants and 288 negative sites. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.
Illumina HiSeq 2500
142
EGAD00001001464
Exome Sequencing.
3 μg of genomic DNA from each sample were sheared and used for the construction of a paired-end sequencing library as described in the paired-end sequencing sample preparation protocol provided by Illumina41. Enrichment of exonic sequences was then performed for each library using either the Sure Select Human All Exon 50 Mb or All Exon+UTRs v4 kits following the manufacturer’s instructions (Agilent Technologies). Exon-enriched DNA was pulled down by magnetic beads coated with streptavidin (Invitrogen), followed by washing, elution and 18 additional cycles of amplification of the captured library. Enriched libraries were sequenced (2 × 76 bp) in one lane of an Illumina GAIIx sequencer or in two lanes of a HiSeq2000 when using pools of eight samples.
-
EGAD00001001465
18 Exomes for discovery set and 60 Targeted panel for prevalence set
Illumina HiSeq 2000
127
EGAD00001001466
Whole Genome sequencing.
2 μg of genomic DNA from each sample was used for the construction of two short-insert paired-end sequencing libraries. Both types of libraries were sequenced in paired-end mode on Illumina GAIIx (2 × 151 bp) using Sequencing kit v4 or Illumina HiSeq2000 (2x101 bp) using TruSeq SBS Kit v3.
-
EGAD00001001467
WGS of 8 trios - affected child and both normal parents
24
EGAD00001001468
PAR-CLIP was performed on the Argonaute-2 protein (AGO2) in four lymphoma cell lines:NamalwaRajiSU-DHL-4SU-DHL-6
Illumina HiSeq 2500
4
EGAD00001001469
RNA-Seq data for 1 T-cell acute leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001470
ChIP-Seq data for 2 plasma cell sample(s). 13 run(s), 12 experiment(s), 12 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001471
RNA-Seq data for 11 Multiple myeloma sample(s). 11 run(s), 11 experiment(s), 11 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
11
EGAD00001001472
ChIP-Seq data for 2 effector memory CD8-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001473
Bisulfite-Seq data for 2 cytotoxic CD56-dim natural killer cell sample(s). 24 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
2
EGAD00001001474
RNA-Seq data for 14 mature neutrophil sample(s). 14 run(s), 14 experiment(s), 14 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
14
EGAD00001001475
DNase-Hypersensitivity data for 1 CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
1
EGAD00001001476
DNase-Hypersensitivity data for 4 CD14-positive, CD16-negative classical monocyte sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
4
EGAD00001001477
RNA-Seq data for 3 neutrophilic myelocyte sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001478
RNA-Seq data for 1 CD8-positive, alpha-beta thymocyte sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001479
Bisulfite-Seq data for 1 memory B cell sample(s). 20 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001480
RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001481
ChIP-Seq data for 15 Acute Myeloid Leukemia sample(s). 75 run(s), 72 experiment(s), 72 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
15
EGAD00001001482
Bisulfite-Seq data for 6 Acute Myeloid Leukemia sample(s). 66 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
6
EGAD00001001483
RNA-Seq data for 1 CD3-negative, CD4-positive, CD8-positive, double positive thymocyte sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001484
Bisulfite-Seq data for 2 erythroblast sample(s). 35 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
2
EGAD00001001485
ChIP-Seq data for 3 Acute Myeloid Leukemia - SAHA sample(s). 11 run(s), 11 experiment(s), 11 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
3
EGAD00001001486
Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
2
EGAD00001001487
ChIP-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 12 run(s), 12 experiment(s), 12 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001488
RNA-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
2
EGAD00001001489
RNA-Seq data for 1 CD4-positive, alpha-beta thymocyte sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001490
ChIP-Seq data for 6 Acute promyelocytic leukemia sample(s). 29 run(s), 27 experiment(s), 27 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
6
EGAD00001001491
Bisulfite-Seq data for 6 inflammatory macrophage sample(s). 83 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
6
EGAD00001001492
RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
4
EGAD00001001493
Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 5 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001494
Bisulfite-Seq data for 1 memory B cells sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001495
ChIP-Seq data for 4 neutrophilic metamyelocyte sample(s). 18 run(s), 12 experiment(s), 12 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
4
EGAD00001001496
RNA-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
2
EGAD00001001497
Bisulfite-Seq data for 2 conventional dendritic cell sample(s). 30 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
2
EGAD00001001498
Bisulfite-Seq data for 5 alternatively activated macrophage sample(s). 79 run(s), 5 experiment(s), 5 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
5
EGAD00001001499
ChIP-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 9 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001500
RNA-Seq data for 2 CD38-negative naive B cell sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
2
EGAD00001001501
RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001502
ChIP-Seq data for 2 germinal center B cell sample(s). 12 run(s), 11 experiment(s), 11 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001503
ChIP-Seq data for 1 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001504
RNA-Seq data for 3 band form neutrophil sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001505
ChIP-Seq data for 7 CD4-positive, alpha-beta T cell sample(s). 39 run(s), 39 experiment(s), 39 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
7
EGAD00001001506
RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
8
EGAD00001001507
Bisulfite-Seq data for 1 mature eosinophil sample(s). 15 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001508
ChIP-Seq data for 9 mature neutrophil sample(s). 48 run(s), 45 experiment(s), 45 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
9
EGAD00001001509
Bisulfite-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001510
Bisulfite-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 36 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
2
EGAD00001001511
ChIP-Seq data for 4 band form neutrophil sample(s). 18 run(s), 17 experiment(s), 17 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
NextSeq 500
4
EGAD00001001512
RNA-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001513
ChIP-Seq data for 5 CD8-positive, alpha-beta T cell sample(s). 26 run(s), 26 experiment(s), 26 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
5
EGAD00001001514
ChIP-Seq data for 4 alternatively activated macrophage sample(s). 22 run(s), 22 experiment(s), 22 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
4
EGAD00001001515
RNA-Seq data for 6 hematopoietic stem cell sample(s). 13 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
6
EGAD00001001516
Bisulfite-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 61 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
3
EGAD00001001517
ChIP-Seq data for 4 neutrophilic myelocyte sample(s). 14 run(s), 14 experiment(s), 14 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
4
EGAD00001001518
ChIP-Seq data for 4 cytotoxic CD56-dim natural killer cell sample(s). 17 run(s), 17 experiment(s), 17 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
4
EGAD00001001519
ChIP-Seq data for 6 naive B cell sample(s). 34 run(s), 28 experiment(s), 28 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
6
EGAD00001001520
RNA-Seq data for 3 mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs) sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001521
RNA-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001522
Bisulfite-Seq data for 2 plasma cell sample(s). 17 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
2
EGAD00001001523
RNA-Seq data for 4 plasma cell sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
4
EGAD00001001524
DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
1
EGAD00001001525
RNA-Seq data for 1 mature eosinophil sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001526
RNA-Seq data for 1 effector memory CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001527
ChIP-Seq data for 3 mature neutrophil - G-CSF/Dex. Treatment (16-20 hrs) sample(s). 18 run(s), 18 experiment(s), 18 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
3
EGAD00001001528
ChIP-Seq data for 1 Leukemia sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001529
Bisulfite-Seq data for 1 precursor B cell sample(s). 6 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001530
Bisulfite-Seq data for 1 Acute Myeloid Leukemia - CTR sample(s). 18 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001531
RNA-Seq data for 1 class switched memory B cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001532
RNA-Seq data for 4 monocyte - None sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
4
EGAD00001001533
ChIP-Seq data for 4 Acute Myeloid Leukemia - CTR sample(s). 21 run(s), 21 experiment(s), 21 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
4
EGAD00001001534
RNA-Seq data for 5 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 23 run(s), 5 experiment(s), 5 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
5
EGAD00001001535
RNA-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
2
EGAD00001001536
ChIP-Seq data for 1 Acute Myeloid Leukemia - MC2884 sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001537
Bisulfite-Seq data for 3 Acute promyelocytic leukemia sample(s). 24 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
3
EGAD00001001538
RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001539
ChIP-Seq data for 2 mature eosinophil sample(s). 12 run(s), 12 experiment(s), 12 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001540
RNA-Seq data for 1 conventional dendritic cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001541
Bisulfite-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 15 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001542
RNA-Seq data for 1 memory B cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001543
RNA-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001544
RNA-Seq data for 10 CD4-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
10
EGAD00001001545
DNase-Hypersensitivity data for 1 alternatively activated macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
1
EGAD00001001546
RNA-Seq data for 1 regulatory T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001547
RNA-Seq data for 1 central memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001548
Bisulfite-Seq data for 2 class switched memory B cell sample(s). 21 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
2
EGAD00001001549
DNase-Hypersensitivity data for 1 Acute Myeloid Leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
1
EGAD00001001550
RNA-Seq data for 7 erythroblast sample(s). 29 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
7
EGAD00001001551
RNA-Seq data for 1 Leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001552
ChIP-Seq data for 9 CD14-positive, CD16-negative classical monocyte sample(s). 56 run(s), 53 experiment(s), 53 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
9
EGAD00001001553
Bisulfite-Seq data for 1 central memory CD8-positive, alpha-beta T cell sample(s). 13 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001554
ChIP-Seq data for 1 adult endothelial progenitor cell sample(s). 8 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001555
RNA-Seq data for 7 Acute promyelocytic leukemia sample(s). 7 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
7
EGAD00001001556
Bisulfite-Seq data for 1 naive B cell sample(s). 5 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001557
ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001558
RNA-Seq data for 5 common lymphoid progenitor sample(s). 20 run(s), 5 experiment(s), 5 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
5
EGAD00001001559
ChIP-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 11 run(s), 11 experiment(s), 11 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001560
DNase-Hypersensitivity data for 2 monocyte sample(s). 4 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
2
EGAD00001001561
RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001562
ChIP-Seq data for 5 Chronic lymphocytic leukemia sample(s). 24 run(s), 23 experiment(s), 23 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
5
EGAD00001001563
Bisulfite-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 15 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001564
Bisulfite-Seq data for 1 regulatory T cell sample(s). 15 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001565
Bisulfite-Seq data for 1 monocytes - T=0days sample(s). 15 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001566
RNA-Seq data for 2 neutrophilic metamyelocyte sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
2
EGAD00001001567
Bisulfite-Seq data for 1 effector memory CD4-positive, alpha-beta T cell sample(s). 15 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001568
ChIP-Seq data for 1 CD8-positive, alpha-beta thymocyte sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001569
ChIP-Seq data for 1 Acute lymphocytic leukemia - CTR sample(s). 7 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001570
ChIP-Seq data for 1 CD3-negative, CD4-positive, CD8-positive, double positive thymocyte sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001571
Bisulfite-Seq data for 4 CD8-positive, alpha-beta T cell sample(s). 56 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
4
EGAD00001001572
RNA-Seq data for 4 monocyte sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
4
EGAD00001001573
DNase-Hypersensitivity data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
3
EGAD00001001574
ChIP-Seq data for 2 erythroblast sample(s). 12 run(s), 12 experiment(s), 12 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001575
Bisulfite-Seq data for 8 macrophage sample(s). 117 run(s), 8 experiment(s), 8 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
8
EGAD00001001576
ChIP-Seq data for 12 macrophage sample(s). 49 run(s), 49 experiment(s), 49 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
NextSeq 500
12
EGAD00001001577
ChIP-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001578
ChIP-Seq data for 1 mesenchymal stem cell of the bone marrow sample(s). 9 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001579
RNA-Seq data for 3 segmented neutrophil of bone marrow sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
3
EGAD00001001580
ChIP-Seq data for 2 monocyte sample(s). 6 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
NextSeq 500
2
EGAD00001001581
DNase-Hypersensitivity data for 16 macrophage sample(s). 20 run(s), 16 experiment(s), 16 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820
Illumina HiSeq 2000
16
EGAD00001001582
RNA-Seq data for 18 macrophage sample(s). 19 run(s), 18 experiment(s), 18 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
18
EGAD00001001583
Bisulfite-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001584
ChIP-Seq data for 1 CD4-positive, alpha-beta thymocyte sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
1
EGAD00001001585
Bisulfite-Seq data for 6 mature neutrophil sample(s). 79 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
6
EGAD00001001586
RNA-Seq data for 4 alternatively activated macrophage sample(s). 6 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
4
EGAD00001001587
Bisulfite-Seq data for 1 germinal center B cell sample(s). 6 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
1
EGAD00001001588
ChIP-Seq data for 4 segmented neutrophil of bone marrow sample(s). 20 run(s), 19 experiment(s), 19 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
NextSeq 500
4
EGAD00001001589
ChIP-Seq data for 7 inflammatory macrophage sample(s). 36 run(s), 36 experiment(s), 36 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
7
EGAD00001001590
Bisulfite-Seq data for 4 CD38-negative naive B cell sample(s). 44 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
4
EGAD00001001591
Bisulfite-Seq data for 7 CD14-positive, CD16-negative classical monocyte sample(s). 101 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820
Illumina HiSeq 2000
7
EGAD00001001592
ChIP-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 14 experiment(s), 14 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
2
EGAD00001001593
RNA-Seq data for 1 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820
Illumina HiSeq 2000
1
EGAD00001001594
ChIP-Seq data for 6 CD38-negative naive B cell sample(s). 20 run(s), 20 experiment(s), 20 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820
Illumina HiSeq 2000
6
EGAD00001001595
ICGC PACA-CA Release 20
Illumina HiSeq 2000
Illumina HiSeq 2500
516
EGAD00001001596
Whole Exome Sequencing data from the germline of the patient as well as the tumors in bone marrow (T-ALL), Liver (Histiocytic Sarcoma) and ileum (non-Langerhans Cell Histiocytosis).
AB 5500xl Genetic Analyzer
4
EGAD00001001598
RNA-sequencing data from teh hT-RPE-MycER cell line after MYC activation and after MINCR knock-down in conditions of MYC ON or OFF
Illumina HiSeq 2500
18
EGAD00001001600
PCR and MiSeq validation for early embryonic substitution candidates from 400 Breast cancer patients.
This dataset contains all the data available for this study on 2015-09-03.
Illumina MiSeq
2
EGAD00001001601
The intersection of genome-wide association analyses with physiological and functional data indicates that variants regulating islet gene transcription influence type 2 diabetes (T2D) predisposition and glucose homeostasis. However, the specific genes through which these regulatory variants act remain poorly characterized. To identify such effector transcripts for T2D and glycemic traits, we generated expression quantitative trait locus (eQTL) data in 118 human islet samples using RNA-sequencing and high-density genotyping.
Illumina HiSeq 2000
118
EGAD00001001602
Illumina HiSeq 2000
1
EGAD00001001607
In this dataset, 16 trios- primary tumor, relapse and corresponding normals- for patients with neuroblastoma are provided. For one patient, more than one relapse was available for the analyses.
Illumina HiSeq 2000
50
EGAD00001001608
Aligned BAM files of whole exome sequencing of 20 syCRCs and 10 normal counterparts. Each sample of 4 patients (S13, S3, S12 and S6) underwent two sequencing rounds.
Illumina HiSeq 2000
Illumina HiSeq 2500
42
EGAD00001001609
Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts
14
EGAD00001001612
After overexpression and knockdown of both described novel miRs nmiR-1 and nmiR-2 in BL cell lines (SU-DHL4 for nmiR-1 and Raji for nmiR-2), we performed regular RNA-Seq (including Mock controls for all cell lines) to identify their direct and indirect downstream mRNA targets.
Illumina HiSeq 2500
16
EGAD00001001613
10
EGAD00001001614
26
EGAD00001001615
10
EGAD00001001616
2
EGAD00001001618
Sequence data from two medullary thyroid carcinoma patients: WGS datasets generated from tumors and matched normal tissues and RNA-Seq from tumors are included.
Illumina HiSeq 2000
Illumina HiSeq 2500
6
EGAD00001001619
miRNA seq data of 43 cases out of dataset EGAD00001000650 (MMML)
43
EGAD00001001620
release_2: ICGC PedBrain: RNA sequencing
Illumina HiSeq 2000
45
EGAD00001001621
release_2: ICGC PedBrain: ChIP-Seq
Illumina HiSeq 2000
31
EGAD00001001622
BBMRI - BIOS project - Freeze 1 - Fastq files
Illumina HiSeq 2000
2199
EGAD00001001623
BBMRI - BIOS project - Freeze 1 - Bam files
2117
EGAD00001001624
release_2: ICGC PedBrain: whole exome sequencing and Target-Seq
Illumina HiSeq 2000
188
EGAD00001001625
release_2: ICGC PedBrain: whole genome sequencing
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
209
EGAD00001001626
RNA-Seq Illumina GAII dataset for the TraIT cell-line use case (added reverse and forward reads).
Illumina Genome Analyzer II
6
EGAD00001001627
This dataset contains RNA sequencing raw data from four parental tumors that were used for classification of gene expression subtypes (Verhaak, Cancer Cell 2010) using ssGSEA.
Illumina HiSeq 2000
4
EGAD00001001628
Illumina HiSeq 2500
Illumina MiSeq
299
EGAD00001001629
Whole-genome somatic rearrangement and point mutation analysis in cell lines with induced telomere fusions.
HiSeq X Ten
20
EGAD00001001630
release_2: ICGC PedBrain: whole genome bisulfite sequencing
Illumina HiSeq 2000
108
EGAD00001001631
Illumina MiSeq
334
EGAD00001001632
miRNA seq data of 13 cases (MMML)
13
EGAD00001001633
BAM files for two WES TRAIP patients
Illumina HiSeq 2000
2
EGAD00001001634
This dataset includes the whole genomes, sequenced to high depth (30x) of 25 individuals from Papua New Guinea. The individuals were chosen from several geographically distinct Papuan groups, focusing on the highland regions: Bundi, Kundiawa, Mendi, Marawaka and Tari.
HiSeq X Ten
25
EGAD00001001635
Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only.study_refcenter AMC
42
EGAD00001001636
Whole-genome sequencing at 4x of 250 samples from the Greek isolatecollection HELIC
Illumina HiSeq 2000
250
EGAD00001001637
Whole-genome sequencing at 1x of samples from the Cretan Greek isolate collection HELIC-MANOLIS. Genome-wide association studies of complex traits have been successful in identifying common variant associations, but a substantial heritability gap remains. The field of complex trait genetics is shifting towards the study of low frequency and rare variants, which are hypothesised to have larger effects. The study of these variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. This work focuses on an isolated population from Crete, Greece. Sequencing is very efficient in isolated populations, because variants found in a few samples will be shared by others in extended haplotype contexts, supporting accurate imputation.
Illumina HiSeq 2000
1003
EGAD00001001638
The HELIC study has been whole genome sequencing individuals from 2 Greek isolatedpopulations at 1x depth. The genotype calling process crucially involves a VQSR stepfollowed by imputation-based refinement. We have been investigating optimal ways toincrease calling accuracy. To aid us in setting appropriate parameters for VQSR and otherQC steps, we have carried out whole exome sequencing of a small number ofHELIC samples.
Illumina HiSeq 2000
5
EGAD00001001639
Low depth (4x) Illumina HiSeq raw sequence data for 2000 Ugandans from various ethno-linguistic group from rural South-West Uganda (related individuals included).
Illumina HiSeq 2000
2000
EGAD00001001642
RIKEN collection of WGS reads of 530 liver cancer and matched blood samples from 260 donors.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
530
EGAD00001001643
RIKEN collection of WGS read of 59 multi-centric liver cancers or intra-haptatic metastasis and matched blood samples from 19 donors.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
59
EGAD00001001644
MicroRNAs (miRs) have been recognized as promising biomarkers. It is unknown to what extent tumor-derived miRs are differentially expressed between primary colorectal cancers (pCRCs) and metastatic lesions, and to what extent the expression profiles of tumor tissue differ from the surrounding normal tissue. Next-generation sequencing (NGS) of 220 fresh-frozen samples, including paired primary and metastatic tumor tissue and non-tumorous tissue from 38 patients, revealed expression of 2245 known unique mature miRs and 515 novel candidate miRs. Unsupervised clustering of miR expression profiles of pCRC tissue with paired metastases did not separate the two entities, whereas unsupervised clustering of miR expression profiles of pCRC with normal colorectal mucosa demonstrated complete separation of the tumor samples from their paired normal mucosa. Two hundred and twenty-two miRs differentiated both pCRC and metastases from normal tissue samples (false discovery rate (FDR) <0.05). The highest expressed tumor-specific miRs were miR-21 and miR-92a, both previously described to be involved in CRC with potential as circulating biomarker for early detection. Only eight miRs, 0.5% of the analysed miR transcriptome, were differentially expressed between pCRC and the corresponding metastases (FDR <0.1), consisting of five known miRs (miR-320b, miR-320d, miR-3117, miR-1246 and miR-663b) and three novel candidate miRs (chr 1-2552-5p, chr 8-20656-5p and chr 10-25333-3p). These results indicate that previously unrecognized candidate miRs expressed in advanced CRC were identified using NGS. In addition, miR expression profiles of pCRC and metastatic lesions are highly comparable and may be of similar predictive value for prognosis or response to treatment in patients with advanced CRC.
Illumina HiSeq 2000
125
EGAD00001001645
Illumina Genome Analyzer II
Illumina HiSeq 2000
28
EGAD00001001646
Fastq files corresponding to RNA-Seq dataset for PTPN1 project (EGAS00001000554)
Illumina Genome Analyzer
Illumina Genome Analyzer II
Illumina HiSeq 2000
10
EGAD00001001655
Genome and transcriptome sequence data from an atypical teratoid rhabdoid tumor patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001656
Genome and transcriptome sequence data from an atypical chronic lymphocytic leukemia patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
2
EGAD00001001657
Genome and transcriptome sequence data from a parotid gland cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001658
Genome and transcriptome sequence data from an odontogenic ghost cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
2
EGAD00001001660
Whole exome sequencing was performed to explore the mutational landscape and potential molecular signature of HPV-positive versus HPV-negative OAC. Four hr-HPV-positive and 8 HPV-negative treatment-naive fresh-frozen OAC tissue specimens and matched normal tissue were analysed to identify somatic genomic mutations
24
EGAD00001001661
Genotype and exome data for an Australian Aboriginal population: a reference panel for health-based research.
72
EGAD00001001662
Whole genome sequences of ACC primagrafts, Histone modification maps and transcription factor binding maps for ACC primagrafts and primary tumors. Processed ChIP-seq data is available on GEO under accession number GSE76465.
Illumina HiSeq 2000
Illumina HiSeq 2500
Illumina MiSeq
NextSeq 500
58
EGAD00001001663
Low coverage (4x-8x) Illumina HiSeq curated sequence data from 3 African populations from the AGV project; 100 Baganda from Uganda (4x), 100 Zulu from South Africa (4x), and 120 Gumuz, Wolayta, Oromo, Somali and Amhara from Ethiopia (8x). Pre-processed, jointly called and filtered with GATK, refined with Beagle3, phased with SHAPEIT2.
1
EGAD00001001664
LGG Epilepsy Cohort WGS
Illumina HiSeq 2000
18
EGAD00001001665
LGG Epilepsy Cohort WXS
Illumina HiSeq 2000
61
EGAD00001001666
LGG Epilepsy Cohort RNA-Seq
Illumina HiSeq 2000
34
EGAD00001001667
Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015
Illumina MiSeq
12
EGAD00001001668
Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015
Illumina HiSeq 2500
12
EGAD00001001669
Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015
Illumina HiSeq 2500
42
EGAD00001001672
Part of RNA sequencing data of Malignant Lymphoma Study (ICGC)
Illumina HiSeq 2000
56
EGAD00001001673
Part of WGS seq data of Maligant Lymphoma study (ICGC)
Illumina HiSeq 2000
Illumina HiSeq 2500
112
EGAD00001001674
Illumina HiSeq 2500
Illumina MiSeq
299
EGAD00001001675
RNA-seq of peripheral blood samples from CLL patients.
Illumina HiSeq 2000
42
EGAD00001001676
Tagmentation-based whole-genome bisulfite sequencing of isolated cell types from healthy controls.
Illumina HiSeq 2000
12
EGAD00001001686
In the autozygosity exome sequencing of Born-in-Bradford samples of Pakistani origin there
is a mother who is homozygous for an apparent truncating stop codon in PRDM9, the gene
responsible for localising recombination during meiosis. We plan to deep sequence mother
and child with X10, and physically phase the mother with PacBio sequencing.
We will use this data to identify recombination locations, and test whether these are
consistent with the known fine scale recombination map.
Data Access is controlled by the Wellcome Trust Sanger Institute DAC and the Born In Bradford Executive Group.
HiSeq X Ten
Illumina HiSeq 2500
2
EGAD00001001687
Illumina HiSeq 2000
56
EGAD00001001688
Illumina HiSeq 2500
34
EGAD00001001689
Illumina HiSeq 2500
27
EGAD00001001690
Tumor-Normal paired samples of PTC
Illumina HiSeq 2000
182
EGAD00001001691
Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide1. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC)2-3. Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 14 ESCC cases and whole-exome sequencing in 90 cases.
Illumina HiSeq 2000
208
EGAD00001001692
Whole exome sequencing of germline DNA was performed and subsequent polymorphisms in genes known and putatively involved in the innate immune response to fungi were identified
Illumina HiSeq 2500
1
EGAD00001001693
Fastq files of RNAseq of 182 samples of biliary tract cancer
Illumina HiSeq 2000
182
EGAD00001001694
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_C
1
EGAD00001001695
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_F
1
EGAD00001001696
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_M
1
EGAD00001001697
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_C
1
EGAD00001001698
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_F
1
EGAD00001001699
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_M
1
EGAD00001001700
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_C
1
EGAD00001001701
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_F
1
EGAD00001001702
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_M
1
EGAD00001001703
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_C
1
EGAD00001001704
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_F
1
EGAD00001001705
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_M
1
EGAD00001001706
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_C
1
EGAD00001001707
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_F
1
EGAD00001001708
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_M
1
EGAD00001001709
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_C
1
EGAD00001001710
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_F
1
EGAD00001001711
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_M
1
EGAD00001001712
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_C
1
EGAD00001001713
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_F
1
EGAD00001001714
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_M
1
EGAD00001001715
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_C
1
EGAD00001001716
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_F
1
EGAD00001001717
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_M
1
EGAD00001001718
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_C
1
EGAD00001001719
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_F
1
EGAD00001001720
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_M
1
EGAD00001001721
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB28_C
1
EGAD00001001722
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB28_F
1
EGAD00001001723
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB28_M
1
EGAD00001001724
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB30_C
1
EGAD00001001725
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB30_F
1
EGAD00001001726
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB30_M
1
EGAD00001001727
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB31_C
1
EGAD00001001728
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB31_F
1
EGAD00001001729
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB31_M
1
EGAD00001001730
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB33_C
1
EGAD00001001731
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB33_F
1
EGAD00001001732
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB33_M
1
EGAD00001001733
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB35_C
1
EGAD00001001734
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB35_F
1
EGAD00001001735
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB35_M
1
EGAD00001001736
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB38_C
1
EGAD00001001737
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB38_F
1
EGAD00001001739
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB40_C
1
EGAD00001001740
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB40_F
1
EGAD00001001741
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB40_M
1
EGAD00001001742
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB41_C
1
EGAD00001001743
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB41_F
1
EGAD00001001744
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB41_M
1
EGAD00001001745
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB42_C
1
EGAD00001001746
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB42_F
1
EGAD00001001747
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB42_M
1
EGAD00001001748
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB43_C
1
EGAD00001001749
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB43_F
1
EGAD00001001750
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB43_M
1
EGAD00001001751
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB44_C
1
EGAD00001001752
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB44_F
1
EGAD00001001753
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB44_M
1
EGAD00001001754
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB4_C
1
EGAD00001001755
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB4_F
1
EGAD00001001756
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB4_M
1
EGAD00001001757
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB50_C
1
EGAD00001001758
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB50_F
1
EGAD00001001759
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB50_M
1
EGAD00001001760
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_C
1
EGAD00001001761
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_F
1
EGAD00001001762
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_M
1
EGAD00001001763
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB52_C
1
EGAD00001001764
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB52_F
1
EGAD00001001765
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB52_M
1
EGAD00001001766
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_C
1
EGAD00001001767
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_F
1
EGAD00001001768
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_M
1
EGAD00001001769
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB57_C
1
EGAD00001001770
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB57_F
1
EGAD00001001771
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB57_M
1
EGAD00001001772
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_C
1
EGAD00001001773
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_F
1
EGAD00001001774
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_M
1
EGAD00001001775
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB60_C
1
EGAD00001001776
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB60_F
1
EGAD00001001777
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB60_M
1
EGAD00001001778
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB62_C
1
EGAD00001001779
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB62_F
1
EGAD00001001780
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB62_M
1
EGAD00001001781
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB8_C
1
EGAD00001001783
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB8_M
1
EGAD00001001784
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW12_C
1
EGAD00001001786
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW12_M
1
EGAD00001001787
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_C
1
EGAD00001001788
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_F
1
EGAD00001001789
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_M
1
EGAD00001001790
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW15_C
1
EGAD00001001792
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW15_M
1
EGAD00001001793
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW18_C
1
EGAD00001001794
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW18_F
1
EGAD00001001795
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW18_M
1
EGAD00001001796
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_C
1
EGAD00001001797
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_F
1
EGAD00001001798
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_M
1
EGAD00001001799
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW22_C
1
EGAD00001001800
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW22_F
1
EGAD00001001802
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW24_C
1
EGAD00001001803
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW24_F
1
EGAD00001001804
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW24_M
1
EGAD00001001805
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW27_C
1
EGAD00001001806
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW27_F
1
EGAD00001001807
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW27_M
1
EGAD00001001808
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW29_C
1
EGAD00001001809
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW29_F
1
EGAD00001001810
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW29_M
1
EGAD00001001811
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW2_C
1
EGAD00001001812
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW2_F
1
EGAD00001001813
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW2_M
1
EGAD00001001814
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW32_C
1
EGAD00001001815
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW32_F
1
EGAD00001001816
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW32_M
1
EGAD00001001817
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_C
1
EGAD00001001818
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_F
1
EGAD00001001819
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_M
1
EGAD00001001820
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_C
1
EGAD00001001821
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_F
1
EGAD00001001822
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_M
1
EGAD00001001823
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_C
1
EGAD00001001824
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_F
1
EGAD00001001825
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_M
1
EGAD00001001826
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_C
1
EGAD00001001827
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_F
1
EGAD00001001828
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_M
1
EGAD00001001829
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_C
1
EGAD00001001830
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_F
1
EGAD00001001831
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_M
1
EGAD00001001833
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW4_F
1
EGAD00001001834
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW4_M
1
EGAD00001001835
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW50_C
1
EGAD00001001836
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW50_F
1
EGAD00001001837
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW50_M
1
EGAD00001001838
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW51_C
1
EGAD00001001839
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW51_F
1
EGAD00001001840
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW51_M
1
EGAD00001001841
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW52_C
1
EGAD00001001842
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW52_F
1
EGAD00001001843
50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW52_M
1
EGAD00001001844
Whole genome sequencing of 64 HER2-Positive Breast Cancer
Illumina HiSeq 2000
128
EGAD00001001845
Leeds Melanoma Cohort
Illumina HiSeq 2000
16
EGAD00001001846
2 BRAFV600E cell lines that have been made resistance to 1. the BRAF inhibitor PLX4720 and 2. the combination therapy of dabrafenib and trametinib seem to have a internal duplication in the kinase domain. We would like to know if this is caused by a translocation.
HiSeq X Ten
4
EGAD00001001847
4C-seq data was generated for regions of interest to confirm enhancer-gene promoter interactions
Illumina HiSeq 2000
1
EGAD00001001848
DDD DATAFREEZE 2014-11-04: 4293 trios - VCF files
-
EGAD00001001849
The genomic sequence of brain expressed miRNA genes was sequenced in Swedish schizophrenia patients
Illumina MiSeq
186
EGAD00001001850
Genomic DNA from Swedish control individuals was pooled. Then the genomic sequence of brain expressed miRNA genes was determined in the pools.
Illumina MiSeq
149
EGAD00001001851
The genomic sequence of brain expressed miRNA genes was sequenced in Belgian epilepsy patients.
Illumina MiSeq
163
EGAD00001001852
Genomic DNA from Belgian control individuals was pooled. Then the genomic sequence of brain expressed miRNA genes was determined in the pools.
Illumina MiSeq
39
EGAD00001001853
In this dataset are the data from :- 17 patients studied by WGS- 49 patients studied by WES- 9 (/49) patients studied by RNASeq at 2 time points- the same 9 patients studied by ERRBS at 2 time points
Illumina HiSeq 2000
199
EGAD00001001854
Exome sequencing of nine PCC/PGL tumors, SF and FFPE samples
18
EGAD00001001856
100
EGAD00001001857
Illumina HiSeq 2000
381
EGAD00001001858
Raw fastq files from WGS sequencing of CLL and matching blood normal for the ICGC Techval Benchmark1 study. Sequence data was provided to multiple centers for independent analysis and comparison.
Illumina HiSeq 2500
2
EGAD00001001859
Raw fastq files for sequence data generated at 5 sequencing centers from a Medulloblastoma sample and matching blood normal control.
Illumina HiSeq 2500
2
EGAD00001001860
19
EGAD00001001861
Exome Sequencing to Define the Landscape of Plasma Cells in Systemic Light chain Amyloidosis
Illumina HiSeq 2000
48
EGAD00001001862
RNA-seq of PDXs
Illumina HiSeq 2000
12
EGAD00001001863
Exome data of PDX models.
Illumina HiSeq 2500
4
EGAD00001001864
DATA FILES FOR PCGP MB WGS - Supersedes (EGAD00001000269)
Illumina HiSeq 2000
76
EGAD00001001865
Sequence Data of total RNA, miRNA, WGB, mRNA, NOMe, Chip (H3K27ac,H3K27me, H3K36me3, H3K4me1, H3K4me3, H3K9me3, Input)Short Desrciption: Epigenetic profiling of human CD4+ memory T cells reveals their proliferative history and argues in favor of a progressive differentiation model driven by epigenetically controlled master regulators.
Illumina HiSeq 2000
21
EGAD00001001869
We report the first combined analysis of whole genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole genome and transcriptome sequence was obtained from 9 anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 years prior to death. Transcriptome analysis revealed increased expression of AR-regulated genes in liver metastases that harbored an AR p.L702H mutation, suggesting a dominant effect by the mutation despite being present in only 1 of an estimated 16 copies per cell. The metastases harbored several alterations to the PI3K/AKT pathway, including a clonal truncal mutation in PIK3CG and present in all metastatic sites studied. The list of truncal genomic alterations shared by all metastases included homozygous deletion of TP53, hemizygous deletion of RB1 and CHD1, and amplification of FGFR1. If the patient were treated today given this knowledge, use of second-generation androgen-directed therapies, cessation of glucocorticoid administration, and therapeutic inhibition of the PI3K/AKT pathway or FGFR1 receptor could provide personalized benefit. Three previously unreported truncal clonal missense mutations (ABCC4 p.R891L, ALDH9A1 p.W89R, and ASNA1 p.P75R) were expressed at the RNA level and assessed as druggable. The truncal status of mutations is critical for actionability, and can only be determined through analysis of multiple sites of metastasis. Our findings suggest that a large set of deeply analyzed cases could serve as powerful guide to more effective prostate cancer basic science and personalized cancer medicine clinical trials.
Illumina HiSeq 2000
7
EGAD00001001870
Deep sequencing of 151 cancer genes in 6 synchronous CRC of 3 patients
Illumina MiSeq
6
EGAD00001001871
Megakaryocytes and erythroblasts derive from the same progenitor cell type but carry out very different functions. In order to understand how the different functional phenotypes arise we have characterised the epigenetic landscape of these cells.
Illumina HiSeq 2500
20
EGAD00001001872
Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases.
This dataset contains all the data available for this study on 2016-01-06.
Illumina HiSeq 2000
333
EGAD00001001873
AML emerges as a consequence of accumulating independent genetic aberrations that direct regulation and/or dysfunction of genes resulting in aberrant activation of signalling pathways, resistance to apoptosis and uncontrolled proliferation. Given the significant heterogeneity of AML genomes, AML patients demonstrate a highly variable response rate and poor median survival in response to current chemotherapy regimens. For the past 4 years we have conducted gene expression profiling on purified bone marrow populations equating to normal haematopoietic stem and progenitor cells from healthy subjects and patients with de novo AML in order to identify AML signatures of aberrantly expressed genes in cancer versus normal. We are now applying a series of bioinformatic methodologies combined with clinical and conventional diagnostic data to establish novel genomics strategies for improved prognostication of AML. Additionally, we use our AML signatures to unravel oncogenic signalling pathway activities in AML patients and test inhibitory drugs for these pathways inn preclinical therapeutic programmes. We consider that superimposing GEP and clinical data for our AML patient cohort with additional data on their mutational status will significantly improve the prognostic power of the study as well as unravel yet unknown mutations associated with aberrant signalling activities of oncogenic pathways.
Illumina HiSeq 2000
215
EGAD00001001874
Illumina HiSeq 2000
16
EGAD00001001876
Genome and transcriptome sequence data from a colorectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study. These data are included in the manuscript entitled, "Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer".
4
EGAD00001001879
A pilot to establish the feasability of using a custom Agilent targeted pulldown of 110 genes implicated in colorectal tumourigensis to sequence for driver mutations in a set of 30 FFPE colorectal adenomas. If successful, we propose to sequence an additional 350 adenomas as part of a MRC research study in order to define the pattern of driver mutations across the spectrum of pathological subtypes including coventional adenomas, serrated adenomas and hyperplastic polyps
Illumina HiSeq 2000
30
EGAD00001001880
RIKEN collection of RNA-seq reads for 458 liver cancer samples and matched normal liver from 247 donors.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
458
EGAD00001001881
RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed.
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
528
EGAD00001001885
January 2016 update of RNA-Seq data (bams, fastqs) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2500
17
EGAD00001001887
Exome sequencing VCF files describing mutations during glioma progression.
82
EGAD00001001889
***THIS DATA CAN ONLY BE USED FOR NON-COMMERCIAL CANCER RESEARCH*** Sequencing of organoid cell lines derived from oesophageal tumour sections taken from patients diagnosed with primary oesophageal cancer who underwent tumour resection surgery.
HiSeq X Ten
9
EGAD00001001891
Whole genome bisulfite sequencing of pedbrain - medulloblastoma
Illumina HiSeq 2000
10
EGAD00001001892
BLUEPRINT Bisulfite-seq and Whole Genome Sequencing of mantle cell lymphoma
Illumina HiSeq 2000
4
EGAD00001001897
15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS
HiSeq X Ten
1482
EGAD00001001898
The study will investigate serial samples from the same patient taken at the time of MGUS or SMM diagnosis, and later at the time of evolution towards MM. Samples will be sequenced by whole genome along with a matched normal to obtain the highest possible amount of information toinvestigate genomic changes at disease evolution. This dataset contains all the data available for this study on 2016-01-27.
HiSeq X Ten
131
EGAD00001001899
HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-driven Medulloblastoma
102
EGAD00001001900
DNA sequencing reads of human adult stem cell cultures from liver, colon and small intestine. Including biopsy or blood samples of the donors.
HiSeq X Ten
Illumina HiSeq 2500
NextSeq 500
61
EGAD00001001901
Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma (MM) with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about molecular mechanism of malignant transformation. We have performed whole exome sequencing together with SNP array analysis in 33 flow-cytometry separated abnormal PC samples of MGUS patients to describe somatic gene mutations and chromosome changes at the genome-wide level. Non-synonymous mutations (NS-SNVs) and copy number alterations (CNAs) were present in 97.0% and in 63.6% of cases, respectively. Importantly, the number of somatic mutations was significantly lower in MGUS compared to MM (p<10-4) and we have identified 6 myeloma significantly mutated genes which are KRAS, NRAS, DIS3, HIST1H1E, EGR1 and LTB in the MGUS dataset. We also found a positive correlation with increasing chromosome changes and somatic mutations. IGH translocations were present in 27.3% of cases comprising t(4;14), t(11;14), t(14;16) or t(14;20) and were in a similar frequency to MM, which corresponded with primary lesion hypothesis. Data from this study showed MGUS is a genetically comprehensive disease, however overall genetic instability is significantly lower compared to MM.
Illumina HiSeq 2000
66
EGAD00001001909
Paired-end whole exome sequenncing (Illumina) of primary enucleated retinoblastoma and matching lymphocyte DNA was performed to find somatic alterations that are related to oncogenesis.
Illumina HiSeq 2500
143
EGAD00001001913
Exome sequencing data for Mesothelioma
Illumina HiSeq 2500
198
EGAD00001001914
RNA-seq data for mesothelioma cell lines after spliceostatin (SSA) or control (DMSO) treatment.
Illumina HiSeq 2000
12
EGAD00001001915
RNA-Seq data for Mesothelioma.
Illumina HiSeq 2000
211
EGAD00001001916
Targeted sequencing using SPET for Mesothelioma.
Illumina HiSeq 2000
207
EGAD00001001917
PacBio data for mesothelioma cell line NCI-H2595.
PacBio RS II
1
EGAD00001001918
Multi-region Illumina whole-exome and/or whole-genome sequencing on tumor regions collected from early-stage NSCLC patients who underwent definitive surgical resection prior to receiving adjuvant therapy.Patients covered by this dataset: L012, L013, L015, L017
Illumina HiSeq 1000
15
EGAD00001001920
TEST3 dataset containing 1 FASTQ file with mRNA reads.
Illumina HiSeq 2500
1
EGAD00001001921
All pituitary samples
Illumina HiSeq 2500
84
EGAD00001001922
RNA-seq from normal human tissues (2 x 250 bp)
Illumina HiSeq 2000
14
EGAD00001001923
RNA sequence data for conditionally reprogrammed cells from patient HUB_5
Illumina HiSeq 2500
1
EGAD00001001925
1461 Neuropathological and clinically characterised cases from the MRC Brain Bank
1461
EGAD00001001926
Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. We performed 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients.
Illumina HiSeq 2000
141
EGAD00001001927
Illumina HiSeq 2000
27
EGAD00001001928
This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Illumina HiSeq 2500
Illumina MiSeq
61
EGAD00001001930
Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens.NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit
Illumina MiSeq
6
EGAD00001001932
HipSci - Healthy Normals - Exome Sequencing - January 2016
Illumina HiSeq 2000
123
EGAD00001001933
HipSci - Healthy Normals - RNA Sequencing - January 2016
Illumina HiSeq 2000
118
EGAD00001001935
Cancer amplicon reads consisting of BAM paired end reads from primary multiple myeloma samples.
Illumina MiSeq
88
EGAD00001001936
Firs 1106 16S rDNA data for the Flemish Gut Flora Project
Illumina MiSeq
1061
EGAD00001001937
Targeted amplicon sequencing of samples as part of the study "Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples. The amplicon panel consists of 48 amplicons in TP53, PTEN, EGFR, PIK3CA, KRAS and BRAF genes as described previously [Forshew, STM 2012]. All libraries were pooled and quantify using DNA 1000 kit on Agilent 2100 Bioanalyzer and KAPA SYBR FAST ABI Prism qPCR Kit (KAPA Biosystems) on 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the supplier's recommendations. Reads were aligned using bwa-mem v0.7.12-r1039 to the 1000 genomes version of human genome build GRCh37, retaining duplicate reads.
Illumina MiSeq
66
EGAD00001001938
Shallow whole-genome sequencing of samples from the study "Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples". DNA from each sample (100ng) was sheared on Covaris S220 (Covaris): duty cycle - 10%, intensity -5.0, bursts per sec - 200, duration - 300 sec, mode - frequency sweeping, power - 23V, temperature -5:5 C to 6 C, water level - 13. Libraries were prepared with the TruSeq Nano DNA LT Sample Prep Kit (Illumina) using a modi?ed protocol - Sample Puri?cation Beads were replaced by Agencourt AMPure XP beads (Beckman Coultier) and size selection after the End Repair was done to remove only the short fragments. Quality and quantity for contructed libraries were assessed with DNA 7500 kit on Agilent 2100 Bioanalyzer and with Kapa Quanti?cation kit (KAPA Biosystems) on 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the supplier's recommendations, respectively. Libraries from 18 barcoded samples were pooled together in equimolar amounts and each pool was loaded on a single lane of a HiSeq Single End Flowcell (Illumina), followed by cluster generation on a cBot (Illumina) and sequencing on a HiSeq 2500 (Illumina) in a single-read 50bp mode. Reads were aligned using bwa-mem v0.7.12-r1039 to the 1000 genomes version of human genome build GRCh37. Picard (http://picard.sourceforge.net) was used to remove duplicate reads.
Illumina HiSeq 2500
60
EGAD00001001939
Mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
Illumina HiSeq 2000
476
EGAD00001001940
Un-mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
Illumina HiSeq 2000
476
EGAD00001001941
Variants derived from mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.
476
EGAD00001001942
We performed target re-sequencing for 1.29 Mb interval of chromosome 9 (chr9:21299764–22590271, hg19). NimbleGen SeqCap EZ choice system was used as a target enrichment method (Roche Diagnostics). A DNA probe set complementary to the target region was designed by NimbleDesign. The libraries were sequenced on the Illumina MiSeq platform with 2×150-bp paired-end module (Illumina). Fastq files for 48 Japanese patients with endometriosis are deposited.
Illumina MiSeq
48
EGAD00001001943
Here, we studied well-phenotyped individuals from the Flemish Gut Flora Project (FGFP, N=1,106, Belgium) and the effect of environments on microbiome. The 69 major significant phenotypes found in this study are provided.
1068
EGAD00001001944
RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project
Illumina HiSeq 2500
42
EGAD00001001947
Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC.
Illumina HiSeq 2000
16
EGAD00001001948
Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC
Illumina HiSeq 2000
16
EGAD00001001949
HipSci - Monogenic Diabetes - Exome Sequencing - April 2015
Illumina HiSeq 2000
1
EGAD00001001950
HipSci - Bardet-Biedl Syndrome - Exome Sequencing - January 2016
Illumina HiSeq 2000
3
EGAD00001001951
HipSci - Monogenic Diabetes - Exome Sequencing - January 2016
Illumina HiSeq 2000
1
EGAD00001001952
HipSci - Bardet-Biedl Syndrome - RNA Sequencing - April 2015
Illumina HiSeq 2000
2
EGAD00001001953
HipSci - Monogenic Diabetes - RNA Sequencing - April 2015
Illumina HiSeq 2000
1
EGAD00001001954
HipSci - Bardet-Biedl Syndrome - RNA Sequencing - January 2016
Illumina HiSeq 2000
3
EGAD00001001955
HipSci - Monogenic Diabetes - RNA Sequencing - January 2016
Illumina HiSeq 2000
1
EGAD00001001956
ICGC Release 21 for PACA-CA from OICR
Illumina HiSeq 2000
Illumina HiSeq 2500
516
EGAD00001001957
March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2500
18
EGAD00001001958
March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2500
17
EGAD00001001959
March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
Illumina HiSeq 2500
20
EGAD00001001960
upcoming publication
Illumina HiSeq 2000
-
EGAD00001001961
Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
4
EGAD00001001962
Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001963
Genome and transcriptome sequence data from a non small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
2
EGAD00001001964
Genome and transcriptome sequence data from a non-small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001965
Genome and transcriptome sequence data from a lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
3
EGAD00001001966
Genome and transcriptome sequence data from a non-small cell lung carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
PromethION
3
EGAD00001001967
Genome and transcriptome sequence data from an adenocarcinoma of right lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
2
EGAD00001001968
Genome and transcriptome sequence data from a non-small cell lung carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
PromethION
2
EGAD00001001969
Genome and transcriptome sequence data from a non-small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
2
EGAD00001001973
Exome sequencing of 184 samples from consanguineous families with different congenital heart defects collected at KAIMRC, Riyadh, Saudi Arabia.
Illumina HiSeq 2000
Illumina HiSeq 2500
179
EGAD00001001977
DDD DATAFREEZE 2014-11-04: 4293 trios - phenotypic and family descriptions
-
EGAD00001001978
This dataset contains FASTQ files for multi-region exome-sequencing of EGFR-mutant lung adenocarcinomas from Asian patient. There are 16 patients and 95 samples in total, including 16 controls and 79 tumors. Multiple runs for each sample, and 368 fastq in total. Please refer to the sample-ID from filename for merging.
Illumina HiSeq 2000
95
EGAD00001001979
This dataset contains BAM file for multi-region exome-sequencing of EGFR-mutant lung adenocarcinomas from Asian patient. There are 16 patients and 95 samples in total, including 16 controls and 79 tumors.
Illumina HiSeq 2000
95
EGAD00001001980
This dataset contains BAM files of targeted Amplicon deep-sequencing data, for validation of the mutations found in WES. There are 16 patients and 95 samples in total, including 16 controls and 79 tumors.
Illumina HiSeq 2500
95
EGAD00001001981
This dataset contains FASTQ files of targeted Amplicon deep-sequencing data, for validation of the mutations found in WES. There are 16 patients and 95 samples in total, including 16 controls and 79 tumors. 140 fastq in total, multiple runs for some of the samples. Please refer to the sample-ID from filename for merging.
Illumina HiSeq 2500
95
EGAD00001001983
Immunoglobulin heavy chain gene high throughput sequencing of paediatric acute lymphoblastic leukaemia samples, for the purpose of MRD on the Illumina MiSeq platform. This dataset contains summary fastq files and raw bcl files from the MiSeq for this study. In the study we identify errors associated with multiplexing that could potentially impact on the accuracy of MRD analysis. We optimise a strategy combining high purity, sequence-optimised oligonucleotides, dual-indexing and an error-aware demultiplexing approach to minimise errors and maximise sensitivity.
Illumina MiSeq
491
EGAD00001001984
To identify recurrent somatic alterations in this unique subset of gastric cancers, whole exome and SNP6 analyses were performed using frozen cancer tissue. The somatic mutation analyses were also performed using blood of the same patients.
Illumina HiSeq 2500
160
EGAD00001001986
This study is meant to gain further knowledge in haematological cancers. Patients samples (mainly DNAs or PCR products) from haematolocical cancer patients will be sequenced, and the outputs will be correlated to their diagnosis and/or prognosis; the findings may also add more insight into the understanding of biology in this type of tumour. We will be sequencing Primary Testicular Lymphomas (PTL) to identify genetic drivers of this rare cancer
Illumina HiSeq 2500
7
EGAD00001001987
March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.
18
EGAD00001001988
Cholangiocarcinoma whole genome sequencing data
HiSeq X Ten
Illumina HiSeq 2000
Illumina HiSeq 2500
118
EGAD00001001991
Meta-genomic sequencing of 1,200 LifeLines-DEEP participants
Illumina HiSeq 2000
1135
EGAD00001001994
CCA targeted sequencing
Illumina HiSeq 2500