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• Dataset-linking-WGS-via-README-for-EGAS00001004884

  This dataset contains 139 Tumor and Control WGS files for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007669

• Demultiplexed FASTQs for each volunteer

  This submission consists of 15 volunteer FASTQs, split by chemistry: Chemistry v1.1: 7 FASTQ sets, one set for each volunteer (RA1-7) Chemistry v2: 16 FASTQ sets, two for each volunteer (RA8-15; FASTQ set 1: Gene Expression (GEX); FASTQ set 2: TCR enrichment (VDJ))

  Dataset EGAD00001007586

• Germline DNA Methylation Associated with Breast Cancer Predisposition

  Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer such as BRCA1 and BRCA2 account for less than 25% of familial cases of breast cancer. Heritable epigenetic modifications, in the form of hypermethylated MLH1 promoter alleles, have recently been shown to promote hereditary nonpolyposis colorectal cancer. We investigated the potential for an epigenetic basis for hereditary breast cancer by performing deep bisulfite sequencing of CpG islands and known promoter regions in germline DNA from 100 familial or early-onset breast or ovarian cancer patients.

  Study phs001699

• dbGaP Collection: Psychiatric Genomics Consortium (PGC) dbGaP Datasets

  This dbGaP Collection includes cases and controls used in the GWAS meta-analysis of neuropsychiatric phenotypes studied by investigators in the Psychiatric Genomics Consortium including major depression, bipolar disorder, attention deficit and hyperactivity disorder, schizophrenia, Tourette Syndrome, and obsessive-compulsive disorder. The consent type for data sets includes general research use as well as phenotype-specific restricted usage. This dbGaP collection was created to facilitate identification of datasets used in PGC analyses in order to expedite the application and ascertainment process for PGC members wishing to access data within the consortium. Non-PGC members may also apply for this dbGaP collection.

  Study phs001254

• PBMC

  Whole-Exome-Sequencing of 5 pooled patients for SNP-based demultiplexing

  Study EGAS50000000654

• SNP Array Data for EGAS00001004666

  SNP Array Data for EGAS00001004666

  Dataset EGAD00010002257

• DATA FILES FOR SJAMLM7

  DATA FILES FOR SJAMLM7

  Dataset EGAD00001000259

• "Usage of small amounts of DNA for Illumina sequencing"

  "Usage of small amounts of DNA for Illumina sequencing"

  Dataset EGAD00001000034

• WGS and WXS files for Dyer ATRX study

  WGS and WXS files for Dyer ATRX study

  Dataset EGAD00001003389

• DATA FILES FOR PCGP SJETP WXS

  DATA FILES FOR PCGP SJETP WXS

  Dataset EGAD00001001248

• Australian genomes

  Mapped data (bam files) for high-throughput whole genome sequence data for 83 modern Aboriginal Australians

  Dataset EGAD00001002001

• DATA FILES FOR Histone Capture bams

  DATA FILES FOR Histone Capture bams

  Dataset EGAD00001000657

• Novel de novo pathogenic variant in the GNAI1 as a cause of severe disorders of intellectual development with autistic features

  Study EGAS00001005346

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Germany

  Study EGAS00001005858

• A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study EGAS00001008123

• Precise reconstruction of the tumor microenvironment using bulk RNA-seq and a unique machine learning-based algorithm trained on artificial transcriptomes

  Study EGAS00001006272

• Novel de novo pathogenic variant in the GNAI1 as a cause of severe disorders of intellectual development with autistic features

  Study EGAS00001005355

• transcriptome analysis of NK cells sorted from PBMCs at baseline and after addition of a T cell dependent bispecific antibody (TDB)

  Study EGAS00001006914

• EGAD00010000391

  Cambridge control samples using a 660K genotyping chip from Illumina

  Dataset EGAD00010000391

• sc-DECISION

  Data derived from PBMC and blood samples for the single cell and bulk RNAseq analysis for the sc-DECISION paper. https://doi.org/10.1101/2025.02.04.25321370

  Dac EGAC50000000642

• Preeclampsia InterPregGen Consortium: GWAS meta-analysis summary statistics for European fetal preeclampsia cases versus controls and GWAS genotype data for European fetal preeclampsia cases

  Study EGAS00001001048

• Dataset for TIX

  All files for TIX individuals

  Dataset EGAD50000000426

• RNAseq for 4 pdx and 1 cell-line

  RNAseq for #1049, #111, #1217, #206, COV362

  Dataset EGAD50000000032

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000853

• DATA FILES FOR SJLGG

  DATA FILES FOR SJLGG

  Dataset EGAD00001000352

• DATA FILES FOR SJLGG

  DATA FILES FOR SJLGG

  Dataset EGAD00001000353

• Reactive Lymph Node Gene Expression Profiling

  Reactive lymph nodes were processed as controls for the study.

  Study EGAS50000001010

• Pulldown_DNA_methylation_study_v2

  Pilot study to set up sequencing protocols for targeted pulldown methylation profiling

  Study EGAS00001000979

• PBMC_dual_10X_kit

  Dual snRNAseq and ATACseq of replicate PBMC samples for 10X beta testing.

  Study EGAS00001004834

• Dataset for "Genomic landscape of oral cancers" (CGI WGS)

  Dataset for "Genomic landscape of oral cancers" (CGI WGS)

  Dataset EGAD00001004339

• DATA FILES FOR SJEWS-WGS

  DATA FILES FOR SJEWS-WGS

  Dataset EGAD00001001020

• DATA FILES FOR PCGP SJMEL WXS

  DATA FILES FOR PCGP SJMEL WXS

  Dataset EGAD00001001246

• DATA FILES FOR PCGP SJMEL RNASEQ

  DATA FILES FOR PCGP SJMEL RNASEQ

  Dataset EGAD00001001247

• DATA FILES FOR PCGP Dyer_iPSC TEBS

  DATA FILES FOR PCGP Dyer_iPSC TEBS

  Dataset EGAD00001001416

• DATA FILES FOR PCGP Dyer_iPSC WGS

  DATA FILES FOR PCGP Dyer_iPSC WGS

  Dataset EGAD00001001415

• DATA FILES FOR PCGP Dyer_iPSC 5hmc

  DATA FILES FOR PCGP Dyer_iPSC 5hmc

  Dataset EGAD00001001418

• McGill EMC Release 4 for assay "H3K9me3"

  McGill EMC Release 4 for assay "H3K9me3"

  Dataset EGAD00001001299

• McGill EMC Release 4 for assay "H3K27me3"

  McGill EMC Release 4 for assay "H3K27me3"

  Dataset EGAD00001001294

• McGill EMC Release 4 for assay "H3K36me3"

  McGill EMC Release 4 for assay "H3K36me3"

  Dataset EGAD00001001295

• McGill EMC Release 4 for assay "H3K4me1"

  McGill EMC Release 4 for assay "H3K4me1"

  Dataset EGAD00001001296

• McGill EMC Release 4 for assay "H3K4me3"

  McGill EMC Release 4 for assay "H3K4me3"

  Dataset EGAD00001001297

• McGill EMC Release 4 for assay "H3K27ac"

  McGill EMC Release 4 for assay "H3K27ac"

  Dataset EGAD00001001298

• BLUEPRINT: DNaseI-seq for monocytes

  DNaseI-seq for monocytes

  Dataset EGAD00001000674

• Dataset for "Genomic landscape of oral cancers" (Illumina WGS)

  Dataset for "Genomic landscape of oral cancers" (Illumina WGS)

  Dataset EGAD00001004356

• Single-Cell Atlas of Common Variable Immunodeficiency shows germinal center-associated epigenetic dysregulation in B cell responses

  Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency. Here the authors perform single cell omics analyses in CVID discordant monozygotic twins and show epigenetic and transcriptional alterations associated with activation in memory B cells.

  Dataset EGAD00001008575

• RNAseq for 8 PDX

  RNAseq for #111, #1177, #206, #201, #29, #931, WO-19, WO-2

  Dataset EGAD50000000116

• DATA FILES FOR PCGP MB WGS - Supersedes (EGAD00001000269)

  DATA FILES FOR PCGP MB WGS - Supersedes (EGAD00001000269)

  Dataset EGAD00001001864

• Linked-reads for Juvenile Pilocytic Astrocytomas

  Matched tumor-normal data for 6 JPAs. Generated using 10X Genomics Linked-reads

  Dataset EGAD00001011114

• Exome and RNA sequencing data for Diffuse Large B Cell Lymphomas

  Exome sequencing data for 1001 DLBCL patients and RNA sequencing data for 775 DLBCL patients

  Dataset EGAD00001003600

• Genomic determination for Homologous Recombination Deficiency (HRD) by shallow Whole Genome Sequencing (sWGS)

  Genomic determination for Homologous Recombination Deficiency (HRD) by shallow Whole Genome Sequencing (sWGS) with shallowHRD (PMID : 32315385) on 55 triple-negative breast cancer Patient Derived-Xenograft (PDX) treated with platinum.

  Study EGAS00001005926