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• BLUEPRINT release August 2016, ChIP-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh38

  ChIP-Seq data for 10 CD14-positive, CD16-negative classical monocyte sample(s). 80 run(s), 76 experiment(s), 76 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002484

• BLUEPRINT release August 2016, ChIP-Seq for central memory CD8-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 3 central memory CD8-positive, alpha-beta T cell sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002450

• BLUEPRINT release August 2016, ChIP-Seq for CD3-positive, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  ChIP-Seq data for 3 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 11 run(s), 11 experiment(s), 11 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002445

• BLUEPRINT release August 2016, ChIP-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 9 CD4-positive, alpha-beta T cell sample(s). 68 run(s), 63 experiment(s), 63 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002444

• Single cell analysis of human lung parenchyma

  Human lung tissue was obtained from deceased organ donors from whom organs were being retrieved for transplantation. Informed consent for the use of tissue was obtained from the donors’ families (REC reference: 15/EE/0152 NRES Committee East of England - Cambridge South). Fresh tissue from the peripheral parenchyma of the left lower lobe or lower right lobe of the lung was excised within 60 minutes of circulatory arrest and preserved in University of Wisconsin (UW) organ preservation solution (Belzer UW® Cold Storage Solution, Bridge to Life, USA) until processing.

  Dataset EGAD00001005065

• The British Autozygosity Populations BioResource (2019-08-14)

  This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. 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/ . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005253

• Investigating the genetics of immunity against Salmonella in humans (2019-09-05)

  This study entails whole genome sequencing of an interleukin (IL)-12 b-1 receptor-deficient individual who presented with a chronic systemic Salmonella Enteritidis infection that did not resolve with standard IFNg and antibiotic treatment. Whole genome sequencing of the patient's parents are also included. 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/ . This dataset contains all the data available for this study on 2019-09-05.

  Dataset EGAD00001005311

• VCF file from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  VCF file from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). BAM files were processed at the CNAG (Barcelona) with their pipeline, including GATK v3.6 for genotyping and other tools such as snpEff for annotating variants, to produce this VCF file with a total of 9,643,070 variants, out of which 7,891,370 are SNVs.

  Dataset EGAD00001005758

• The identification of genetic vulnerabilities in head and neck cancers for the development of novel therapies (2020-01-15)

  CRISPR/Cas9 lethality screens in a set of Asian head and neck cancer cell lines to identify novel targets. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005784

• Hereditary Cancer Diagnostics with I2HCP gene panel

  Germline blood DNA sequencing data generated in routine diagnostics of hereditary cancer using the I2HCP gene panel (~135 genes). There are 130 samples sequenced in a MiSeq machine and 108 sequenced in a HiSeq machine. There is a partial overlap between those two sets, meaning that some samples were sequenced in both machines. There is a strong enrichment in samples with copy-number variants (CNV), both single- and multi-exon, since this dataset was compiled for a benchmarking effort of CNV calling tools for genetic diagnostics.

  Dataset EGAD00001006171

• 252 human breast cancer samples in WGS and WES

  We analyzed chromothripsis in 252 human breast cancers from two patient cohorts (149 metastatic breast cancers, 63 untreated primary tumors, 29 local relapses, 11 longitudinal pairs) using whole-genome and whole-exome (paired) sequencing. A lot of the WGS samples were sequenced on Illumina HiSeq X-Ten using Illumina TruSeq Nano DNA. For exome sequencing Agilent_SureSelect_V5+UTRs has been used (sequencing on Hiseq2000, Hiseq2500 and Hiseq4000). For exome sequencing Agilent_SureSelect_V5+UTRs has been used (sequencing on Hiseq2000, Hiseq2500 and Hiseq4000).

  Dataset EGAD00001007563

• Exploring the heterogeneity of sarcoma using single cell sequencing

  Multi region samples are collected from patients, with consent, immediately after resection of the tumour. Samples are digested and sorted using FACS as single cells into lysis buffer. Cells are then stored until further processing for G&T-seq. After sequencing, we will explore intra-tumour heterogeneity using computational approaches to integrate RNA and DNA data onto the tumour phylogeny 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/ .

  Dataset EGAD00001006786

• Single cell sequencing of human normal breast myoepithelial cells

  The dataset includes 6 FASTQ files with single cell transcriptome sequencing data of normal breast myoepithelial cells from ducts and TDLUs derived from reduction mammoplasties from three patients. Chromium Single Cell 3’ Reagent Kit v2 or v3 (10x Genomics) were used for processing of cells, whereafter sequencing was performed using the Illumina® NextSeq500/550 High Output Kit v2. Cell Ranger was used for generating FASTQ files and files from different lanes were concatenated prior to uploading the data to EGA.

  Dataset EGAD00001008468

• Development and Validation of a Prognostic and Predictive 32-Gene Signature for Gastric Cancer

  We applied this signature to a 567-patient GC cohort to establish genomic-based molecular subtypes and then used a support vector machine to build a molecular subtype-based risk-scoring model. Both source code and supplementary datasets for risk score prediction are available at https://github.com/hwanglab/Yonsei_gastric_cancer_32genes.

  Dataset EGAD00001008091

• DDD_1 hypermutated individual

  CRAM files and VCF for DDD_1 and their parents. Also de novo mutations file for hypermutated DDD_1 child as described in the manuscript ‘Genetic and chemotherapeutic influences of germline hypermutation’ by Kaplanis et al. which will be published in Nature shortly.

  Dataset EGAD00001008497

• Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer

  Whole genome sequencing from two resectable patients with pancreatic cancer for both normal and tumour tissue samples; whole exome sequencing from the two resectable patients and five unresectable patients of peripheral blood mononuclear cells and blood plasma (1-5 time points per patient), and whole exome sequencing of plasma samples from three chronic pancreatitis patients.

  Dataset EGAD00001008593

• LCM-ATACseq on human lung macrophages

  In this study we employed Laser Capture Microdissection (LCM) for the multimodal profiling of lung macrophages cell populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (~100 cells) were collected from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation), and processed for ATAC-seq.

  Dataset EGAD00001008693

• LCM-RNAseq on human lung macrophages

  In the reported study, we employed Laser Capture Microdissection (LCM) for the transcriptome profiling of lung macrophages cells populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (100 cells each) were collected by LCM from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation) and processed for RNA-seq.

  Dataset EGAD00001008694

• Normal sample for patient SA495

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA495

  Dataset EGAD00001009372

• Normal sample for patient SA425

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA425

  Dataset EGAD00001009371

• Normal sample for patient SA423

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA423

  Dataset EGAD00001009370

• Normal sample for patient SA300

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA300

  Dataset EGAD00001009369

• Normal sample for patient SA291

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA291

  Dataset EGAD00001009368

• Normal sample for patient SA289

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA289

  Dataset EGAD00001009367

• Normal sample for patient SA286

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA286

  Dataset EGAD00001009366

• Normal sample for patient SA280

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA280

  Dataset EGAD00001009365

• Normal sample for patient SA239

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA239

  Dataset EGAD00001009364

• Normal sample for patient SA679

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA679

  Dataset EGAD00001009379

• Normal sample for patient SA680

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA680

  Dataset EGAD00001009380

• Normal sample for patient SA681

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA681

  Dataset EGAD00001009381

• Normal sample for patient SA682

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA682

  Dataset EGAD00001009382

• Normal sample for patient SA683

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA683

  Dataset EGAD00001009383

• Normal sample for patient SA678

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA678

  Dataset EGAD00001009378

• Normal sample for patient SA677

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA677

  Dataset EGAD00001009377

• Normal sample for patient SA673

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA673

  Dataset EGAD00001009373

• Normal sample for patient SA676

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA676

  Dataset EGAD00001009376

• Normal sample for patient SA674

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA674

  Dataset EGAD00001009374

• Normal sample for patient SA675

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA675

  Dataset EGAD00001009375

• TARGET-seq+ single-cell transcriptome sequencing

  Single-cell whole transcriptome sequencing data for bone marrow samples from 9 cases with clonal hematopoiesis and 4 control samples. The TARGET-seq+ protocol was used to generate plate-based 3' transcriptome data. For details on cell sorting and the TARGET-seq+ protocol see the methods section of the manuscript. One FASTQ file is provided per cell. Cells are named with their plate and well IDs and the subject ID. Empty wells (no-cell controls) are named "blank". Corresponding genotyping files use the same naming without the "_transcriptome" suffix.

  Dataset EGAD00001011175

• Sequencing data for oesophageal and related samples - Abbas et al (WGS)

  Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (WGS for 1397 samples)

  Dataset EGAD00001011196

• Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

  This dataset comprises FASTQ files for single-cell RNA-seq and single-cell ATAC-seq data. These data were generated using 10x Genomics' multiome kit. In this cohort, there are 25 samples from 17 human cancer patients.

  Dataset EGAD00001015782

• UCSF Sebaceous Carcinoma DAC for review of sequence data release from manuscript in Nature Communications, based in the UCSF Departments of Dermatology and Pathology

  Dac EGAC00001000850

• Inherited Corneal Dystrophies - Institute of Ophthalmology, University College London (IoO, UCL)

  DAC created for access to data published by Dr. Alice E Davidson

  Dac EGAC50000000213

• ITER-FIISC Data Access Committee

  DAC for whole-genome variant calling data of individuals from the study of allergic diseases in the Canary Islands.

  Dac EGAC50000000180

• Mechanism of Decitabine response in MDS/AML patients

  Data access agreement for access to scRNASeq data of serial AML/MDS patients undergoing decitabine treatment.

  Dac EGAC50000000550

• Exome sequencing for identifying point mutations driving M haemophilum susceptibility

  To understand non tuberculous Mycobacterial susceptibility

  Study EGAS50000001076

• UROMOL 2020 - RNA-seq data for validation

  Total RNAseq data from 47 patients with NMIBC.

  Study EGAS00001005050

• SMPaeds cfDNA lcWGS

  Low coverage whole genome sequencing (0.5-4X) for cfDNA collected from blood plasma.

  Dataset EGAD50000000782

• BreastCancer_Miroarrays

  Genotyping array data for breast cancer and matched normal mammary gland samples

  Dataset EGAD00010002251

• Genotypes_Agta

  Genotype data for Agta hunter-gatherers Philippines

  Dataset EGAD00010002140