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• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW50_C

  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

  Dataset EGAD00001001835

• Sequencing files for "A Unifying Paradigm for Transcriptional Heterogeneity and Squamous Features in Pancreatic Ductal Adenocarcinoma."

  Files from DNA and RNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues.

  Dataset EGAD00001005519

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days B-glucan, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days B-glucan 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002522

• The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer

  The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer includes 538 bam files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD00001005339

• Validation data for the SV analysis package: GRIDSS, PURPLE, LINX

  Validation data containing sequencing data of 13 samples. An hybrid capture approach was used to validate findings of both Manta and GRIDSS for the samples in the validation set. The dataset also contains the reference sequences used.

  Dataset EGAD00001005525

• Human tumour ChIP-seq.

  We profiled 16 patient tumour samples by ChIP-seq. H3K27ac and Input are provided for 16 samples and H3K27me3 is provided for 14 samples. Among the 16 samples, 9 are G34WT and 7 are G34R/V. The raw fastq or bam files are provided.

  Dataset EGAD00001006100

• Genomic and transcriptomic data of glioma specimens

  Dataset consists of 207 glioma samples of WHO grades II, III and IV. Dataset consists 182 tumor derived genomic data of ~700 cancer-related and epigenetic-related genes with matched blood samples for 48 specimens. Dataset also consists transcriptomic data for 105 specimens. In total 335 bam files were deposited.

  Dataset EGAD00001006299

• GWAS for IgA Nephropathy

  IgA nephropathy (IgAN) is a common form of immune-mediated glomerulonephritis characterized by glomerular deposition of IgA-containing immune complexes and manifesting with hematuria, proteinuria, and often kidney failure. This dataset is from a genome-wide association study (GWAS) designed to identify novel genetic risk loci for IgAN. In this dataset, seven cohorts were genotyped by Illumina Multi-Ethnic Global Array, consisting of 3,337 IgAN cases and 2,177 healthy controls of European and East Asian ancestries. Three of the provided cohorts were genotyped by Illumina HumanImmuno Chip, which are composed of 2007 cases of IgAN of European ancestry. These cohorts were used in the GWAS meta-analysis, as described in the manuscript entitled "GWAS defines pathogenic signaling pathways and prioritizes drug targets for IgA nephropathy" (Nature Genetics 2022, in press).

  Study phs000431

• Comprehensive Molecular Analysis of Colon Cancer for the Identification and Validation of New Biomarkers

  This study aims to identify diagnostic and prognostic biomarkers in colon cancer and to study understand the complex genomic, genetic and epigenetic relationships with a multiomic approach. The study includes tumor and paired normal mucosa of 100 colon cancer patients diagnosed at stage II, untreated and with microsatellite stable tumours. Also 50 normal mucosa samples from healthy donors are included as reference. The samples have been analysed for gene expression with Affymetrix U219 array (available at GEO GSE44076), SNP/CNV with the Affymetrix 6.0 Human SNP array, for DNA methylation with the Illumina 450K array. Small RNAs were sequenced with the Solid technology and 42 of the tumours and paired normal mucosa DNA were whole exome sequenced with Illumina Genome Analyzer.

  Study EGAS00001002453

• Transcriptional and DNA binding profiling of CEBPE in REH acute lymphoblastic leukaemia cells using shRNA RNA-Seq and ChIP-Seq

  ChIP-Seq - CEBPE - REH. The ETV6/RUNX1 translocated acute lymphoblastic leukaemia cell line. REH was used to perform ChIP-Seq using a CEBPE antibody. Cells were fixed in 1% formaldehyde for 10mins, prior to preparation of chromatin using Active Motif Express ChIP-IT. 2ug of antibody (anti CEBPE Atlas Antibodies HPA002928)was added to 25ug of chromatin O/N at 4C with rotation. Duplicate reactions were pooled and purified. 10ng of ChIP’d and input DNA used for Illumina NGS preparation (NEBNext ChIP-Seq Library kit; New England Biolabs), CEBPE and Input DNA ChIP samples were sequenced on a MiSeq using 150bp Kit v3 paired end and a HiSeq 2500 using 2x101 version 4 paired end (Illumina) respectively. Reactions performed in duplicate. shCEBPE RNA-Seq - REH. REH cells were lentivirally transduced with a pTRIPZ shRNA vector for transcriptional profiling of CEBPE. Two controls (empty and non-targeting) and two CEBPE shRNAs (V3THS_150517(A13), V3THS_404312(G3) Dharmacon, GE) were transduced into REH cells. Cells were treated with 1ug/ml doxycyclin for 144hrs and total RNA purified using Qiagen RNeasy. Knock down of CEBPE was validated by qRT. RNA integrity >7.7 for all samples. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illuimna HiSeq 2500 using 2x101 version 4 paired end chemistry. 3 biological replicates of each samples were prepared.

  Dataset EGAD00001004084

• Open Targets 020 Epigenomes of Cell Lines (2018-10-23)

  There is currently a drive to establish cell based assay systems of greater human biological and disease relevance through the use of well characterised transformed cell lines, primary cells and complex cellular models (e.g. co-culture, 3D models). However, although the field is gaining valuable experience in running more non-standard & complex cell assays for target validation and compound pharmacology studies, there is the lack of a systematic approach to determine if this expansion in cell assay models is reflected in increased human biological and disease relevance. The increasing wealth of publically available transcriptomic, and epigenome (ENCODE and Epigenome Roadmap) data represents an ideal reference mechanism for determining the relationship between cell types used for target & compound studies to primary human cells and tissues from both healthy volunteers & patients. The CTTV020 epigenomes of cell line project aims to generate epigenetic and transcriptomic profiles of cell lines and compare these with existing and newly generated reference data sets from human tissue and cell types. The aim is to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients. Multiple cell types commonly used within research have been grouped according to biology. Examples include erythroid, lung epithelial, hepatocyte cell types and immortalised models of monocyte / macrophage biology. 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 please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-10-23.

  Dataset EGAD00001004415

• Associate Vice President for Research Administration & Director

  Dac EGAC00001003114

• DAC for Duke-NUS genomic sequencing projects

  Dac EGAC00001000256

• DAC for Whole Genome Sequencing of ASD quartet families

  Dac EGAC00001000288

• The Shlien Lab, The Hospital for Sick Children

  Dac EGAC00001000289

• DAC for IGMM / Usher Institute, University of Edinburgh

  Dac EGAC00001000365

• DAC for esophageal squamous cell carcinoma genomic data

  Dac EGAC00001000444

• MacFeeters Hamilton Centre for Neuro-Oncology Research (MHC-NOR)

  Dac EGAC00001000510

• DAC for Dave Lab, Duke University

  Dac EGAC00001000538

• DAC for Single Cell Transcriptomics of Colorectal Cancer

  Dac EGAC00001000550

• Data access committee for BAMS exome sequencing data.

  Dac EGAC00001000583

• DAC for DCM-cases (149 human DCM samples)

  Dac EGAC00001000673

• DAC for DCM-controls (113 human non-DCM samples)

  Dac EGAC00001000674

• DAC for AA HCC patient from National Taiwan University

  Dac EGAC00001000708

• Institut Jules Bordet Data Access Committee for EGAS00001002685 study

  Dac EGAC00001000748

• Data Access Committee for Tumor Progression Study at Karolinska Institute

  Dac EGAC00001000778

• DAC for Institute of Human Genetics, Bonn, AGA Project

  Dac EGAC00001000831

• DAC for study Hypothalamic transcriptome in Prader-Willi syndrome

  Dac EGAC00001000869

• DAC for Genomic landscpae of Chordoid Glioma study

  Dac EGAC00001000906

• Data Access Committee for the Medulloblastoma Host Genome Study

  Dac EGAC00001000910

• Data Access Committee for Niigata-NIG collaborative work

  Dac EGAC00001000955

• DAC for study Non-coding RNAs in Breast Cancer

  Dac EGAC00001001090

• DAC for Peritoneal Mesothelioma sequencing study (LAGA-VPC)

  Dac EGAC00001001093

• ASAN Center for Cancer Genome Discovery Data Access Commitee

  Dac EGAC00001001285

• ASAN Center for Cancer Genome Discovery Data Access Commitee

  Dac EGAC00001001391

• DAC for RNA-Seq Transcriptomic CD4+ T data from EGAS00001004152

  Dac EGAC00001001462

• The data usage policy for epigenomic profile of diverse cancer

  Dac EGAC00001001540

• Englander Institute for Precision Medicine - WCM - Yale - Duke DAC

  Dac EGAC00001001777

• Single cell multi-omics (scNOVA) group for CLL)

  Dac EGAC00001001880

• DAC for Smart-seq2 kidney glomerular single cell project

  Dac EGAC00001001895

• DAC for de-methylation of the FOXP3-TSDR study

  Dac EGAC00001001902

• Data access Commitee for anti-PD1 in HCC data

  Dac EGAC00001002404

• Data Access Committee for Niigata-NIG collaborative work

  Dac EGAC00001002429

• Data Access Committee for Niigata-NIG collaborative work

  Dac EGAC00001002469

• DAC for tFL with PMBL GE signature Exome samples

  Dac EGAC00001002474

• Center for International Blood and Marrow Transplant Research (CIBMTR)

  Dac EGAC00001002536

• Single cell multi-omics (scNOVA) group for Skin fibroblast

  Dac EGAC00001002833

• AmsterdamUMC Data Access Committee for the EPIC-CD study

  Dac EGAC00001003480

• Genomic and transcriptome analysis for intrahepatic cholangiocarcinoma

  Study EGAS00001006007

• DAC for RNAseq data in B cell malignancies

  Dac EGAC50000000399

• Test GWAS Data for Training and Computational Benchmarking

  Study EGAS00001007914

• Data Access Committee for Triple Negative Breast Cancer dataset

  Dac EGAC00001003584

• The EMC-HEMA-SCN DAC for severe congenital neutropenia data

  Dac EGAC00001003590

• DAC for GWAS of Phenytoin-Induced SJS/TEN in Thailand

  Dac EGAC00001003602

• Data Access Commitee for schizophrenia and control cases sequencing data

  Dac EGAC00001002810

• The data access committee for TIGIT in MCL with CART

  Dac EGAC00001003167

• DAC for study characterisation of CpG islands in human tissues

  Dac EGAC00001000068

• DAC for the MDC-LSR-SAHLSIS ischemic stroke study

  Dac EGAC00001000226

• DAC for integrated genomics of metastatic prostate cancer

  Dac EGAC00001000230

• English Longitudinal Study for Ageing (ELSA) Genetic Data Access

  Dac EGAC00001000270

• Data access committee for the head and neck project

  Dac EGAC00001000374

• DAC for the Singapore Integrating Omics Study

  Dac EGAC00001000685

• DAC for AA HCC patient from Chang Gung Memorial Hospital

  Dac EGAC00001000707

• European Bank for induced pluripotent Stem Cells (EBiSC)

  Dac EGAC00001000768

• DAC for the project on epigenetic dysregulation in tuberculosis

  Dac EGAC00001000909

• Data Access Committee members for NETWork! project

  Dac EGAC00001000930

• Ludwig Data Access Committee for the Study of Oesophageal Cancer

  Dac EGAC00001000978

• Fecal Microbiota Transplantation for refractory immune checkpoint inhibitor-associated colitis

  Dac EGAC00001001021

• Search for bacteria in neural tissue from amyotrophic lateral sclerosis

  Dac EGAC00001001058

• DAC for WGS data Romanians and Roma/Rroma (Romania)

  Dac EGAC00001001184

• DAC for Analysis of mechanisms of CD19- relapse in CARPALL study

  Dac EGAC00001001257

• DAC for Genome-Wide Scans of Signals of Selection

  Dac EGAC00001001351

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001001483

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001001485

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001001615

• Epichaperome - Englander Institute for Precision Medicine - Weill Cornell Medicine DAC

  Dac EGAC00001001890

• DAC for the study EGAS00001005773

  Dac EGAC00001002411

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001002437

• DAC for COPD human sputum 16s rRNA gene sequencing data

  Dac EGAC00001002779

• EGAD00010000819

  Summary statistics from meta-analysis for BP phenotypes

  Dataset EGAD00010000819

• Data access committee for sequencing data at Kyoto University

  Dac EGAC50000000045

• Data access committee for neural retina and retinal organoid data

  Dac EGAC50000000019

• bed_files

  Bed files as whitelist for Tapestri Insights analysis

  Dataset EGAD00010002560

• DAC for access to array genotypes from the PREGO biobank.

  Dac EGAC00001003484

• Centre for Drug Repurposing and Medicines Research Data Access Committee

  Dac EGAC00001002764

• XClone for analyzing somatic copy number alterations Data Access Committee

  Dac EGAC00001003492

• Single cell multi-omics committee for CK-AML

  Dac EGAC00001003353

• Developmental and Stem Cell Biology department - Hospital for Sick Children

  Dac EGAC00001002951

• Anne Eugster, Center for Regenerative Therapies Dresden, TU Dresden

  Dac EGAC50000000315

• WGBS and oxBS-seq for APL

  Study EGAS00001005610

• Data access committee for sequencing data generated by Wyatt Lab

  Dac EGAC50000000538

• University of Melbourne Centre for Cancer Research (UMCCR) Data Access Committee

  Dac EGAC00001003567

• AGLCD sequencing data

  sequencing datasets for AGLCD patient

  Dac EGAC50000000852

• MK Clinical Trial DAC

  DAC for MK Clinical Trial Data

  Dac EGAC50000000677

• NHLBI's Collection of Datasets for General Research Use (Public Posting of Genomic Summary Results: Allowed)

  This collection contains all of NHLBI's authorized individual-level genomic datasets currently in dbGaP that are approved for General Research Use (GRU) and have no further limitations beyond those outlined in the model Data Use Certification Agreement. Genomic Summary Results (GSR) sharing is allowed (unrestricted) or not applicable. To request access to this study collection, select phs003132 in the dbGaP Authorized Access System.

  Study phs003132

• MicroRNA Biomarkers for Prediction of Preeclampsia

  Maternal serum was collected between 17-28 weeks gestation. Samples were obtained from the high-risk Placental Study at the University of California, San Diego (n=48) and from the average-risk Proteomic Assessment of Preterm Risk (PAPR) Study at Sera Prognostics (n=164). RNA was extracted from 500 microliter of maternal serum using the miRNeasy Micro kit (Qiagen). NEBNext Small RNAseq Library Preparation Kit was used for library construction.

  Study phs002016

• Large Scale Meta-analysis Characterizes Genetic Architecture for Common Psoriasis-associated Variants

  The genotypes obtained from the Affymetrix Biobank Plus array constituted one of eight Caucasian datasets used in a large genome-wide meta-analysis of the association of psoriasis cases versus unaffected controls. With a combined effective sample size of > 39,000 individuals, this study identified 16 new psoriasis loci achieving genome-wide significance, increasing the total number of identified psoriasis loci for European-ancestry populations to 63.

  Study phs001306

• T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis

  Data Access Committee means the following members of the Institute of Experimental Immunology, UZH, and investigators of the publication, to which the Data Access refers and who are responsible for making the data access decisions for the genotype and gene expression generated by UZH or respectively the epigenetic data, which had been generated at Karolinska Institute. Christian Münz, PhD; Co-Director of Institute of Experimental Immunology, University of Zurich Roland Martin, MD; Affiliated Group Leader (to Institute Münz) of Institute of Experimental Immunology Institute of Experimental Immunology Ivan Jelcic, PhD, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland Maja Jagodic, PhD, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden

  Dac EGAC50000000464

• Long-read sequencing for cell-free DNA analysis (human)

  In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Cell-free DNA from plasma samples of 31 pregnant women at different trimesters, 6 hepatitis B carriers, and 8 patients with hepatocellular carcinoma were sequenced with the two platforms.

  Study EGAS00001006328

• Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS).

  The datasets includes 21 samples from 7 families with Bosma arhinia microphthalmia (BAMS). For details of the study please refer to the manuscript "De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development", Nature Genetics 2017. Each sample was exome sequenced and the family ID in sample description refers to the Individual ID in Supplementary figure 2 of the manuscript.

  Study EGAS00001002193