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• Whole genome bisulfite sequencing on 10 multiple myeloma cases

  Whole genome bisulfite sequencing on 10 multiple myeloma cases. Data quality control and adaptor-trimmed were performed with the Trimomatic tool. Paired-reads were mapped to the hg19 human reference with methylCtools aligner.

  Dataset EGAD00001007821

• AML-PMP miRNA-Seq

  miRNA libraries of the AML-PMP project were sequenced on the Illumina HiSeq 2000 instrument, approximately 16 samples per HiSeq lane, to a median depth of 5.7 million reads per library.

  Dataset EGAD00001009772

• Woodcock et al TenMenDeep Study EGA Dataset A

  Woodcock et al TenMenDeep EGA Dataset A. These are Illumina based deep sequencing data based on bait capture sequencing. See Woodcock et al methods for more detail. Note: the Amplicon sequencing data type is selected because the EGA Website currently has no option to select Bait Capture Sequencing or similar.

  Dataset EGAD00001005381

• Targeted Sequencing of Human Myeloid Malignancies

  This study involves targeted sequencing of samples from myeloid malignancies at different timepoints to assess clonal evolution of malignancy a. 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 EGAD00001002225

• Microinjection of hIPSC-derived intestinal organoids with Salmonella Typhimurium

  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/

  Dataset EGAD00001001363

• LabExMI_SNP_genotyping

  Genotype data for 5,699,237 genotyped and imputed SNPs in the 816 healthy donors of the Milieu Intérieur cohort

  Dataset EGAD00010001489

• Epigenetic Intratumor Heterogeneity and Clonal Evolution in Aggressive Prostate Cancer

  Our study investigated the spatial epigenome variation within 5 aggressive prostate adenocarcinomas.

  Study EGAS00001000682

• Genetics of male infertility in India

  The study comprises of whole exome and genome files of infertile males of Indian origin.

  Study EGAS00001008171

• Mosaic Colorectal Metastasis

  A comparison of the somatic variation present in a primary colorectal tumour and three different liver metastases from the same patient.

  Dataset EGAD00001000948

• Evaluation of the immune effects of tumor-treating electric fields (TTFields) in GBM patients

  Study EGAS00001005392

• atrial appendage miRNA-seq in non-, paroxysmal and persistent atrial fibrillation

  64 left atrial appendages from patients without atrial fibrillation (AF) undergoing cardiac surgery, patients with paroxysmal AF and with persistent AF (~20 per group). Trizol RNA isolation, size selection, single end miRNA sequencing on 4 lanes of illumina NextSeq 500. Provided are FastQ files, one per lane per sample. Additional data (e.g. clinical characteristics, RIN values etc.) can be provided upon request. The same RNA samples (62) were used for transcriptome sequencing. Results from transcriptome sequencing are stored in the EGA database and are managed by the same DAC.

  Dataset EGAD00001007694

• The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways

  69 OAMZL patients were sequenced on the Illumina platform. The data files are available in BAM format.

  Dataset EGAD00001011067

• Epigenome-wide association study of cocaine use disorder in postmortem human brain tissue

  Analysis of cocaine use disorder (CUD) associated epigenome-wide DNA methylation (DNAm) alterations in human postmortem brain tissue of Brodmann Area 9. Tissue samples from N=21 CUD cases and N=21 individuals without CUD originating from the Douglas Bell Canada Brain Bank (DBCBB) were included. Epigenome-wide DNAm was investigated using the Illumina Infinium MethylationEPIC array.

  Dataset EGAD00010002396

• Whole-Exome Sequencing Plasma Control Samples for Benchmarking

  This study contains whole-exome sequencing plasma and HapMap (12877, 12878) control samples for bioinfomatic bencmarking. Plasma samples contain variations in the genes KRAS, NRAS, PIK3CA, and EGFR, including insertions and deletions, at 0.0%, 0.1%, 1.0%, and 5.0%.

  Study EGAS50000000565

• Cohort B tumor exome sequencing

  Cohort B includes IDH-wild type, EGFR amplified, surgically derived glioblastoma tissue samples from male and female individuals. Tumor DNA was isolated from FFPE tissue. Both tumor and germline DNA are present for each sample in the overall dataset.

  Study EGAS50000000955

• Coloured individuals from South Africa

  Genome-wide genotype array data (H3Africa_2017_20021485_A2 and H3Africa_2019_20037295_B1 arrays) of 152 individuals from different locations in South Africa and self-identified as Coloured. From the sites of Graaff-Reinet, Genadendal, Greyton, Nieu-Bethesda, Kranshoek, Prince Albert and Oudtshoorn.

  Study EGAS50000000352

• Immunoglobulin Heavy-Chain locus in Multiple Sclerosis (n=4)

  Peripheral-blood or monocyte DNA from two healthy donors and two individuals with multiple sclerosis were sequenced on a PromethION-2 Solo (P2 Solo) instrument using R10.4.1 flow-cells and the Ultra-Long DNA Sequencing Kit (SQK-ULK114). For each participant we provide FASTQ reads (on-target), and haplotype-resolved assemblies of the complete IGH locus (~1.3 Mb) in FASTA format.

  Dataset EGAD50000001517

• DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  The dataset contains 18 samples. It includs 12 paired whole genome sequencing, and 2 matched short read and long read RNA sequencing of liver organoids, 2 paired RIP RNA sequencing samples. All the experiments were performed on Illumina platform with raw reads stored in fastq format or bam format.

  Dataset EGAD50000001625

• RNA fastq files and mutation annotation files

  This dataset contains the results of both RNA sequencing and DNA sequencing. For RNA sequencing, it includes data from 12 samples derived from 9 patients, provided as raw sequencing files in FASTQ format. For DNA sequencing, it contains mutation information obtained from targeted panel DNA sequencing, including data from 35 individuals in the mutation annotation file (MAF) format.

  Dataset EGAD50000001768

• Genetic landscape of pediatric ependymoma

  We performed whole-genome sequencing of 42 paired tumor/normal EPD genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000254

• Genetic landscape of pediatric Rhabdomyosarcoma

  We performed whole-genome sequencing of 13 paired tumor/normal Rhabdomyosarcoma genomes and analyzed somatically acquired single nucleotide variations SNVs, insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000256

• Genetic landscape of pediatric Osteosarcoma

  We performed whole-genome sequencing of 37 paired tumor/normal OS genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000263

• Whole genome sequencing of pediatric BCR-ABL1 positive acute lymphoblastic leukemia

  We performed whole-genome sequencing of 18 paired tumor/normal BCR-ABL1+ leukemia genomes and analyzed single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the tumor and normal genomes

  Study EGAS00001000253

• SJCRH Patient-derived orthotopic xenografts of pediatric brain tumors

  Primary patient pediatric brain tumors from patients treated at SJCRH were implanted and amplified only in the brain of immunocompromised mice without tissue culture steps and referred as patient-derived orthotopic xenografts (Smith et al, Acta Neuropathologica, 2020).

  Study EGAS00001005533

• IGPP Consortium GWSS Summary Results Data

  The data are the aggregate results from an IGPP Consortium genome-wide survival study, showing overall risk for Parkinson disease progression associated with each variant in a longitudinal cohort study. 11.2 million deeply imputed variants in 3,821 PD patients who were prospectively tracked with 36,123 visits over a median of 6.7 years from disease onset (inter-quartile range, 4.2 years) were analyzed. Data include hazard ratio, SNP ID, and P value.

  Dataset EGAD00001007060

• CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  Dataset EGAD00001007938

• Paired ONT and downsampled Illumina cfDNA dataset

  The dataset contains 12 lung cancer plasma cfDNA samples, 8 bladder cancer and 2 healthy control urine cfDNA samples collected in EDTA collection tubes. Shallow WGS was performed using both Oxford Nanopore Technologies' MinION platform with an R9.4.1 flow cell and the SQK-PBK004 kit (22 files) and Illumina Novaseq platform with an S4 flow cell in PE150bp configuration (2x22 files).

  Dataset EGAD00001009392

• RNA-sequencing of six Pilocytic astrocytoma tumors

  Total stranded TruSeq RNA sequencing by Illumina of six tumor samples from six cases of pediatric Pilocytic astrocytoma. The data is published in the following paper: Tomic TT, Olausson J, Wilzen A, Sabel M, Truve K, Sjogren H, Dosa S, Tisell M, Lannering B, Enlund F, Martinsson T, Aman P, Abel F. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One. 2017 Apr 27;12(4):e0175638.

  Dataset EGAD00001003143

• Whole exome sequencing (WES)

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains whole exome sequencing data of 37 tumor/normal pairs from the screening cohort plus an additional relapse tumor of one of those 37 patients. Data was generated on Illumina HiSeq 2000 device in paired-end mode and is stored in BAM file format.

  Dataset EGAD00001011324

• RNA-seq data

  This dataset contains 200 RNA-seq bam files (142 SLE, 58 healthy individuals). RNA libraries were prepared with the Illumina TruSeq sample preparation kit and were sequenced on Illumina HiSeq2000. 49 bp paired-end reads were mapped to the GRCh37 reference human genome using the GEM mapper.This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity

  Dataset EGAD00001005037

• The genomic landscape of lung adenocarcinoma in East Asians

  We performed exome sequencing of 210 and transcriptome sequencing of 181 LUADs of Chinese patients. For more details, please see publication "Genomic landscape of lung adenocarcinoma in East Asians" by Chen J. et. al. in Nature Genetics 2020. https://www.nature.com/articles/s41588-019-0569-6.

  Study EGAS00001002941

• RNA-Seq Profiles from the CheckMate-577 Clinical Trial

  The dataset contains RNAseq profiles of 386 patients from the CheckMate-577 (CA209-577) clinical trial whose ICF allows data deposition into a public repository. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNA was analyzed using the Illumina TruSeq RNA Access method for library preparation, followed by sequencing on the Illumina NovaSeq platform with a 50bp paired-end strategy and a target read depth of 50M per sample. Fastq files are included.

  Dataset EGAD50000002394

• RNA-seq following miR-130a overexpression (OE) in human CD34+cord blood cells

  We performed RNA-seq on CD34+ human cord blood (CB) cells transduced with Control or miR-130a OE lentiviruses to identify differentially expressed genes. Sorted CD34+ cells from 3 independent cord blood pools were transduced with lentiviruses containing mOrange (mO) reporter gene. mO+ cells were sorted 3 days post-transduction and RNA was harvested for library preparation and sequencing.

  Study EGAS00001005868

• Multi-region targeted Sequencing data of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region targeted re-sequencing on a total of 140 samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 2 relapsed neuroblastoma.

  Dataset EGAD00001008156

• Sequencing of Cervical Cancer

  Precision mapping of genetic alterations in cancer can enable better selection of therapies and improved outcomes when combined with new sequencing diagnostics. We describe whole-exome sequences from cervical adenocarcinomas and paired normal samples in Hong Kong Chinese women. These data uncover a heterogeneous genomic landscape but identify commonly aberrant loci including FAT1, ARID1A, ERBB2 and PIK3CA that may provide a focus for the development of individualized targeted therapies for Chinese women with cervical adenocarcinoma.

  Study phs000723

• scRNA-seq of CD4+ T cells from blood and tumor of NSCLC patients

  This study explore the CD4+ T cells diversity in paired blood and tumor of 5 different NSCLC patients. After FACS-sorted of Tregs (DAPI- CD45+ CD4+ CD25hi CD127lo) and Tconvs (DAPI- CD45+ CD4+CD25lo CD127lo/hi), cells were mixed in equal proportion (fifty/fifty ratio) and processed with 10X Chromium (10X Genomics) gene expression kit (3 bloods and 2 tumors) or immunoprofiling kit (2 bloods and 3 tumors) and sequenced using Illumina platforms.

  Study EGAS50000000293

• NEC

  This multi-centre, non-randomized, open-label, phase II trial (NCT03016338), assessed niraparib monotherapy (cohort 1, C1), or niraparib and dostarlimab (cohort 2, C2) in patients with recurrent serous or endometrioid endometrial carcinoma. The primary endpoint was clinical benefit rate (CBR). Secondary outcomes were safety and objective response rate (ORR). Translational research was an exploratory outcome. Potential biomarkers were evaluated in archival tissue by immunohistochemistry and next generation sequencing panel. Feasibility of liquid biopsy by ctDNA was assessed.

  Study EGAS00001007013

• An IL-1β driven neutrophil-stromal cell axis fosters a BAFF-rich microenvironment in multiple myeloma

  This depository contains data from two bulk RNA sequencing experiments: 1) Bulk RNA sequencing data of peripheral blood neutrophils from healthy donors cultured with a) human adipose-derived stromal cells (ADSC) as a model for mesenchymal stromal cells (MSC), and b) IL-1β stimulated ADSC as a model for inflammatory MSC as found in multiple myeloma (MM). 2) Bulk RNA sequencing data from ADSCs cultured a) without stimuli, b) with recombinant human IL-1β, c) with supernatant from iMSC-like cells, d) with neutrophils previously cultured with MSC, e) with neutrophils previously cultured with iMSC, f) with neutrophils previously cultured with iMSC in the presence of anti-human IL-1β or g) with neutrophils previously cultured with iMSC in the presence of an isotype control.

  Dataset EGAD00001010080

• Whole Exome Sequencing in Familial Parkinson Disease

  We have an ongoing study that has recruited families having at least a sibling pair with Parkinson disease (PD). Families have been screened for mutations in known PD causative genes (LRRK2, parkin, etc). Following review of families without a causative mutation, we selected families for whole exome sequencing that had the strongest history of PD and with the most definitive diagnosis. All families have at least 3 affected family members who were evaluated as part of this study. Only affected family members were included for whole exome sequencing.

  Study phs000376

• Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET)

  STARNET is a genetics of RNA expression study of multiple disease-relevant tissues obtained from living patients with cardiovascular disease. Tissue samples are obtained from blood, atherosclerotic-lesion-free internal mammary artery (MAM) and atherosclerotic aortic root (AOR), subcutaneous fat (SF), visceral abdominal fat (VAF), skeletal muscle (SKLM), and liver (LIV) during open thorax surgery of 600 coronary artery disease (CAD) patients. All patients gave written informed consent. The inclusion criterion was eligibility for coronary artery by-pass graft (CABG) surgery. Patients with other severe systemic diseases, such as active systemic inflammatory disease or cancer, were excluded. The primary clinical end points were the SYNTAX score based on the extent of coronary atherosclerosis assessed from preoperative angiograms. The STARNET patients are Caucasians (31% females); 32% had diabetes, 75% had hypertension, and 67% had hyperlipidemia; and 33% had an MI before age 60. By New York Heart Association criteria, 45% were class I, 42% class II, 9% class III, and 1% class IV. TYPES AND RNA SEQUENCING: 566 DNA genotype and 3577 RNA-seq profiles from seven tissues from 600 STARNET CABG patients passed quality control (on average 511 RNA-seq profiles/tissue). DNA was genotyped with the OmniExpress Exome array (Illumina, ~900k SNPs) and imputed to a total of 14,098,063 DNA variant calls (6,245,505 with minor allele frequency >5%). The STARNET subjects mainly overlap with Caucasian of Northern European (Finnish) descent. RNA sequencing was performed using the HighSeq2000 platform, poly-A (LIV, SKLM, VAF, SF and blood) and ribo-zero (AOR, MAM) protocols with 50-100 bp read lengths, single end to 15-30 million read depth.

  Study phs001203

• Independent development of lymphoid and histiocytic malignancies from a shared early precursor

  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).

  Dataset EGAD00001001596

• BRCA1 secondary splice-site mutations

  BRCA1 splice isoforms d11 and d11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out mutation-containing exons, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers of BRCA1 exon skipping remain undetermined. We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with BRCA1 exon 11 frameshift mutations for splice isoform expression and therapy response.

  Study EGAS50000000022

• Whole-exome sequencing and RNA-seq data of paired normal-tumour samples from MMR-proficient early-onset colorectal cancer patients

  This study aims to identify novel hereditary colorectal cancer predisposition genes by performing whole-exome sequencing and RNA-seq of paired normal colonic mucosa and colorectal cancer samples from 19 patients diagnosed with MMR-proficient colorectal cancer at an age of 50 years or younger. Both whole-exome and RNA sequencing were performed on the Illumina platform.

  Study EGAS50000001296

• Skeletal muscle transcriptomic comparison between long-term trained and untrained men and women

  Published study: https://www.cell.com/cell-reports/fulltext/S2211-1247(20)30789-0 To investigate the influence of lifelong exercise training on human metabolism, we generated global skeletal muscle transcriptomic data from long-term endurance (9 men, 9 women) and strength (7 men) trained individuals. These data were compared with healthy age-matched untrained controls (7 men, 8 women).

  Study EGAS00001004367

• Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms

  Pancreatic neuroendocrine neoplasms (PNENs) are biologically and clinically heterogeneous neoplasms. We used a multi-omics approach to uncover the molecular factors underlying this heterogeneity and derive a potential disease classification. Transcriptomic analysis of 84 primary PNEN specimens, drawn from two cohorts (n = 36 and 48), identified four subgroups with distinct molecular profiles. Whole-exome sequencing revealed subgroup-enriched mutational differences.

  Study EGAS00001005024

• Detection of cancer cell transcriptomes

  Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.

  Dataset EGAD00001009005

• The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer (CIN3+)

  We analysed DNA methylation at >850,000 CpG sites across the genome using the Illumina EPIC array in a total of 1,254 cervical liquid-based cytology samples from cases of screen-detected histologically verified CIN1-3+ (98% hrHPV-positive) and population-based control women free from any cervical disease (100% hrHPV-positive). We developed the WID-CIN-test which is a DNA methylation signature consisting of 5,000 CpG sites.

  Study EGAS00001005078

• Whole exome sequencing in patients with ALS and concomitant FTD lacking the C9orf72 repeat expansion

  Dac EGAC00001000656

• Effect of aging on chromatin accessibility and gene expression in immune cells, The Jackson Laboratory

  Dac EGAC00001000721

• The data access committee for genome-wide cell-free DNA fragmentation in patients with cancer

  Dac EGAC00001001180

• DAC Committee for the "PIK3CA mutation in a case of CTNNB1 mutant sinonasal glomangiopericytoma" study

  Dac EGAC00001002371

• Somatic pathogenic variants in the normal mammary gland of sporadic breast cancer patients.

  Dac EGAC00001002391

• The European MAPPYACTS trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

  Dac EGAC00001003276

• Genomic validation of the revised Bethesda criteria in terms of pathogenesis and oncologic significance

  Study EGAS00001003959

• Genotype data from 'Evidence of the interplay of genetics and culture in Ethiopia'

  Study EGAS00001005171

• DAC-2023-07-05-Ritz (DAC-007)

  Full description of the dataset and all necessary information on metadata may be found under (https://zenodo.org/records/11237107): DAC-2023-07-05-Ritz (DAC-007), raw data in EGA, metadata in Zenodo (https://zenodo.org/records/11237107)

  Dataset EGAD50000001147

• single cell transcriptomics fastq files from PBMC of long COVID patients

  This dataset consists of 8 patients' data fastq files. 4 in each LR1 and 4 in LR2. the dataset was generated using 10X genomics and novaseqX.

  Dataset EGAD50000001730

• The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers

  WES and clonality characterization of different timepoints in HER2-negative primary breast cancers receiving neoadjuvant eribulin therapy.

  Study EGAS00001004953

• Spectrum and significance of MYC and BCL2 mutations in DLBCL

  We analyzed the spectrum and clinical significance of MYC and BCL2 mutations in 347 DLBCL cases from population-based cohort of BC, Canada.

  Dataset EGAD00001003140

• Multiomics characterisation of Long Covid

  We generated 10X, droplet-based paired snRNAseq+snATACseq (Multiome) of patients suffering from Long Covid. In total, we included 31 patients. Single nuclei libraries are genetically multiplexed across donors, genotype files are available to enable demultiplexing. Phenotype sheets provide information of pools/donors as well as donor phenotype.

  Dataset EGAD50000000202

• Long read mRNA sequencing of blood cells exposed to different immune stimuli

  Long-read (PacBio) RNA sequencing dataset of in vitro stimulated PBMC cells. 5 samples consisting of 1 RPMI control and 4 stimulus conditions (lipopolysaccharide (LPS), polyI-polyC, S. aureus and C. albicans) all originating from one donor. Files are raw BAM format files generated by Sequel 2 machine.

  Dataset EGAD00001009998

• Myeloid gene panel or whole exome sequencing data on blood and bone marrow of 15 individuals with germline RUNX1 mutations to characterize additional somatic mutations.

  This dataset consists of 20 fastq files in total from exome and myeloid gene panel sequencing of 15 carriers of germline RUNX1 mutations from 10 different families.

  Dataset EGAD00001006010

• Antibody Repertoires in CVID

  The data consist of the DNA sequences of antibody gene rearrangements from peripheral blood human B cells of subjects with Common Variable Immune Deficiency (CVID) and healthy controls subjects.

  Study phs000934

• Latency and interval therapy affect the evolution in metastatic colorectal cancer

  The cohort of 15 patients included ten patients with available tissue from the primary tumor and ≥1 metastatic site, four patients with pairs of metastases only, and one patient with an anastomotic recurrence five years after initial resection of the primary tumor

  Dataset EGAD00001005226

• Cardiogenics_Custom_Pools - Agilent SureSelect

  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.

  Dataset EGAD00001000397

• Nimblegen

  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.

  Dataset EGAD00001000398

• GSA reference

  reference whole exome sequence serving as a reference of individuals. Includes the raw GSa files and the called variants in vcf format merge for all individuals (S1-S5).

  Dataset EGAD50000000481

• ORCADES 15x (2019-07-23)

  15x whole genome sequencing in samples from the isolated population of Orkney. This dataset contains all the data available for this study on 2019-07-23.

  Dataset EGAD00001005194

• bam files Targeted BS

  Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015

  Dataset EGAD00001001667

• BAM Files MBD-SEQ

  Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015

  Dataset EGAD00001001668

• ST dataset from subcortical white matter MS lesions (CA & CI) and controls

  This dataset contains the FASTQ files, the correspondent H&E pictures with the fiducial frames and the json files that were used for the spatial transcriptomic analysis in our paper (n=19). Within the json files names, one can find the information about the slide name (V11M111-111) and the capture area (A1) for each sample.

  Dataset EGAD50000000520

• The Haplotype Reference Consortium

  The Haplotype Reference Consortium (HRC) will create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts. By combining together multiple cohorts, the reference panels produced by the project will be as large as possible in terms of both number of haplotypes, and numbers of variants. This will increase the accuracy of the genotype imputation, especially at low-frequency variants, and the number of imputable variants, thus increasing the power of GWAS.

  Study EGAS00001001710

• RNA-seq data of CRC-PDX tumors after drug treatment

  We obtained bulk RNAseq data of CRC-PDX tumors after administration of drug or vehicle to clarify the mechanisms of action.

  Dataset EGAD50000000849

• Dataset for LCPlus_WGS

  WES/WGS sequencing data of 56 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009275

• Bone Cancer - Rare Types Whole Genome

  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.

  Dataset EGAD00001000785

• MT amplicon sequencing reads of 217 Egyptian individuals

  This data set contains for 217 Egyptian individuals the amplicon sequencing reads mapping to chrM. These were subsequently used for haplogroup assignment.

  Dataset EGAD00001006040

• Whole-genome sequences of single-cell derived clonal samples and bulk blood samples from human

  Human single cells were clonally expanded by culture and whole-genome sequenced. This dataset includes 334 clonal samples and 7 blood bulks from seven individuals (DB2, DB3, DB5, DB6, DB8, DB9, DB10). We extracted genomic DNA materials from clonally expanded cells and matched peripheral blood using DNeasy Blood and Tissue kits (Qiagen) according to the protocol. DNA libraries for WGS were generated by an Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) from 1 µg of genomic DNA materials. WGS was performed on either the Illumina HiSeq X platform or the NovaSeq 6000 platform to generate mean coverage of 25.2X for 374 clonally expanded cells and 94.8X for 7 matched blood tissues.

  Dataset EGAD00001007032

• EFFORT/LifeLines control human stool metagenomes (46 samples)

  Metagenomes of stool samples from 46 Lifelines control subjects (no antimicrobial use in the past three months before sampling, no occupational lifestock contact). Samples were sequenced and analysed as part of the EFFORT project and derived from the LifeLines cohort from the Northern parts of the Netherlands. http:///www.lifelines.nl.

  Dataset EGAD00001005443

• Exome sequencing of a novel cervical cancer cell line

  In this work, we establish and characterized a low-passage cervix cancer cell line from a Brazilian patient with squamous cell carcinoma. The dataset contains three samples from the same patient (blood, tumor tissue and the primary cell line). The technology used was exome sequencing and the file type available is fastq files.

  Dataset EGAD00001004480

• DAC for Human exome sequencing data from three family members reported in the publication

  Germline variants in UHRF1 are associated with multi-locus imprinting disturbance in humans and mice. Eguzkine Ochoa, Ilona Zvetkova, Sunwoo Lee, Nozomi Takahashi, Benoit Lan-Leung, Emma Hobson, Mahmoud Issa, Bryndis Yngvadottir, France Docquier, Fay Rodger, Dounia Foster-Hall, Graeme Clark, Ana Toribio, Ezequiel Martin, Leonardo Bottolo, Anne C Ferguson-Smith, Wolfgang Fischle, Miguel Constancia, Eamonn R Maher

  Dac EGAC50000000710

• Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA

  This dataset contains the CRAM files of the samples used for the article "Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA" published in Genome Medicine.

  Dataset EGAD00001009816

• Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform

  Ultra low coverage sequencing results from the project 'Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform'. Sequencing data of sample NA12877 and NA12878 generated from 3 nanopore sequencing runs are included in this dataset.

  Dataset EGAD00001004052

• TCS validation of 11 lung adenos

  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.

  Dataset EGAD00001000985

• Longitudinal RNA-seq in a twin cohort

  The dataset consists of 232 RNA-seq samples (whole blood) obtained from healthy female from the TwinsUK adult registry cohort. The samples were obtained at two time points separated on average by 22 months.

  Dataset EGAD00001002068

• Sequencing component for the whole genome methylation analysis in PBMCs and cell subset pilot study DAC

  Dac EGAC00001000096

• JAK/STAT signaling promotes the emergence of regenerative cell states in ulcerative colitis

  Study EGAS00001007098

• CB

  CB: Aligned sequences used in the error modeling study

  Dataset EGAD00001005261

• Nuclease deficiencies alter plasma cell-free DNA methylation profiles (Mouse samples)

  The dataset contains sequencing data in wildtype, Dnase1-deficient and Dnase1l3-deficient mice. We performed 2 x 75bp paired-end whole genome bisulfite sequencing of pooled plasma cell-free DNA (cfDNA) and buffy coat genomic DNA. The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases.

  Dataset EGAD00001007751

• Bulk RNAseq of cultured fibroblasts

  Fastq files from bulk RNAseq of fibroblasts after culture and facs sorting (N=9). Sorted FAP+ CAF cells RNAs were extracted using Qiagen miRNeasy Kit (Qiagen, #217004) according to the manufacturer's instructions. Verification of RNA integrity and quality was performed using the Agilent RNA 6000 nano Kit (Agilent Technologies, #5067-1511). cDNA libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina, #20020594) followed by sequencing on NovaSeq (Illumina).

  Dataset EGAD50000000323

• Validation of Exome-sequencing of S7RE-iPSC lines

  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/

  Dataset EGAD00001001449

• This dataset contains fastq and BAM data from female adipose tissue.

  Here we have from 64 samples, their corresponding fastq and bam files. The study group consisted of 17 obese women with normal glucose tolerance and 15 obese women with T2DM classified according to WHO standards. The groups were matched for age, BMI and waist circumference. All the women had been morbidly obese (BMI>40 kg/m2) for at least five years.

  Dataset EGAD00001002202

• Oxidative phosphorylation is a key ontogenetic feature of monocyte immunometabolism promoting myeloid differentiation after birth

  The dataset consists of 12 samples of monocytes, which were analyzed using RNA-sequencing (RNA-seq). These samples were categorized into four distinct groups, each comprising three samples. The dataset was designed to investigate the transcriptomic and metabolic profiles of monocytes across different age groups and stimulation conditions. 3 neonatal controls, 3 neonatal LPS stimulated, 3 adult controls and 3 adult LPS stimulated samples.

  Dataset EGAD00001011340

• Misoprostol-induced high fever GWAS study

  Genome-wide association (GWAS) meta-analysis study of misoprostol-induced fever was conducted on two South American cohorts (Argentina and Ecuador). DNA was collected from blood of women who were screened for postpartum haemorrhage (PPH) and administered misoprostol were included in the study. Genotypes were acquired from the Global Screening Array (Illumina). Meta-analysis of these cohorts was completed using METAL software.

  Study EGAS00001005455

• Benchmarking dataset for ProSolo, a probabilistic single nucleotide caller for single cell DNA sequencing data

  This is the dataset used in the benchmarking of ProSolo, a new probabilistic single nucleotide variant caller for single cell DNA sequencing data that provides control over the false discovery rate of different single cell events at genomic sites (e.g. alternative allele presence or allele dropout). It provides the whole exome sequencing data used in assessing ProSolo's performance that is not available elsewhere, namely bulk whole exome sequencing data of a patient with a constitutional mismatch repair defect (MSH6-) and their parents and siblings, a bulk whole exome sample of granulocytes from that patient and 5 single granulocytes whole exome sequenced after whole genome amplification.

  Dataset EGAD00001005929

• RNAseq of samples from CLL patients treated with idelalisib in vivo

  The dataset contains RNA sequencing data from 18 paired samples of 9 CLL patients treated with idelalisib in vivo (median time on therapy 4 weeks; range 2-5 weeks).

  Dataset EGAD50000000878

• Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) tumor patient

  Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015291

• COLORS in IBD: Whole exome sequencing of early onset IBD patients

  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.

  Dataset EGAD00001001316

• Single-cell profiling of neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade

  This dataset includes 406 samples from non small cell lung cancer patients treated with neoadjuvant anti-PD-1. The Single Cell 5’ V(D)J and 5’ DGE kits (10X Genomics) were used to capture immune repertoire information and gene expression from the same cell in an emulsion-based protocol at the single cell level. Libraries were generated and sequenced on an Illumina NovaSeq instrument using 2x150bp paired end sequencing.

  Dataset EGAD00001007728

• sWGS of matched patient and PDX ovarian tumour tissues

  This dataset contains 8 .bam files of shallow WGS (~0.1×) from fresh frozen tumour tissues of four matched patients and first generation PDX models. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008650

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW20_F

  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

  Dataset EGAD00001001797