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• Bulk transcriptomics of Human High-Grade-B-Cell-Lymphomas differentiated according to IGH status

  GCB DLBCL MB2 DE and HGBCL-DH-BCL2(-BCL6) cases classified according to IGH status in IGH+ or IGH-undetectable

  Dataset EGAD50000001524

• Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population

  We mapped microRNA expression quantitative trait loci by quantifying microRNA expression using small RNA sequencing.

  Study JGAS000504

• Star-based RNA count files

  To ellucidate gene activity in mRCC, RNA Sequencing data was generated as part of the EuroTarget study. Star aligner 2.7 was used to generate count files

  Dataset EGAD50000002296

• KIT-dependent and -independent genomic heterogeneity of resistance in gastrointestinal stromal tumors - TORC1/2 inhibition as salvage strategy

  The mutational status of GIST analyzed with a broad sequencing approach (WES, RNAseq)

  Study EGAS00001003405

• Expanding the neurodevelopmental phenotypes of individuals with de novo KMT2A variants

  We have sequenced four samples to identify variants in KMT2A gene. Three samples were sequenced with WGS, one was sequenced by WES (Patient2).

  Dataset EGAD00001004838

• DIME

  Shotgun sequencing data from subject as baseline and after 4 weeks of daily doses of low, medium or high CFU Eubacterium hallii L2-7. The strain contained in the drink "Ela" was also sequenced.

  Dataset EGAD00001004849

• non-IVF MeDIP-seq bam files

  Bam files consisting of aligned MeDIP-seq reads from cord blood cells and cord blood mononuclear cells of twins not conceived through in vitro fertilisation

  Dataset EGAD00001003159

• Exome profiling of desmoplastic small round cell tumors (DSRCTs)

  Exome sequencing of frozen resected specimens of desmoplastic small round cell tumors (DSRCTs). Four patients have specimens from multiple tissue sites included in this dataset.

  Dataset EGAD00001006394

• 666PG genomic rearrangements

  Genomic rearrangement calls generated using Delly in VCF format from the CPCGene 666PG study

  Dataset EGAD00001006146

• Dataset to study clonal evolution in TCF3:PBX1 patient SJE2A066 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJE2A066 with 69 high quality cells sequenced (62 blast and 7 normal)

  Dataset EGAD00001011329

• Dataset to study clonal evolution in TCF3:PBX1 patient SJE2A063 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJE2A063 with 80 high quality cells sequenced (75 blast and 5 normal)

  Dataset EGAD00001011328

• Dataset to study clonal evolution in TCF3:PBX1 patient SJE2A067 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJE2A067 with 78 high quality cells sequenced (73 blast and 5 normal)

  Dataset EGAD00001011330

• ATAC-seq of spermatogonia

  Raw sequencing reads of ATAC-seq of spermatogonia in FASTQ format, comprising 6 samples sequenced on the Illumina HiSeq 4000 platform.

  Dataset EGAD00001007759

• PrevANZ RNAseq dataset

  Whole blood samples collected at baseline and week 12 in PAXgene Blood RNA tubes. RNA sequencing on the Illumina NovaSeq 6000 System generated 150 base pair length paired end reads.

  Dataset EGAD00001011069

• Dataset to study clonal evolution in iAMP21 patient SJBALL030072using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJBALL030072with 66 high quality cells sequenced (61 blast and 5 normal)

  Dataset EGAD00001010288

• Infiltrative and drug-resistant slow-cycling cells support metabolic heterogeneity in glioblastoma

  Glioblastoma patient derived Fast/Slow cycling cancer stem cell RNA sequencing. Consists of 3 patient cell lines and 6 files

  Dataset EGAD00001004380

• Genetic architecture of male infertility in India

  The dataset consists of whole exome and genome sequencing data from infertile males and his parent(s) and/or sibling(s)

  Dataset EGAD00001015606

• RNAseq of LC2AD with AD80 or DMSO

  RNAseq of LC2AD with AD80 or DMSO Plenker et al., Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer

  Dataset EGAD00001003316

• Breast RNA Sequencing

  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.

  Dataset EGAD00001001340

• BASIS RNA Sequencing

  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.

  Dataset EGAD00001001341

• EBV-AID project

  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.

  Dataset EGAD00001001458

• Ovarian cancer sequencing dataset

  Sequencing data from patients with Ovarian cancer. Data utilised in the 'Enhanced detection of circulating tumor DNA by fragment size analysis' manuscript (Mouliere et al, 2018)

  Dataset EGAD00001004939

• Single cell sequencing in CNS autoimmune disease

  RNA, T cell receptor and B cell receptor single cell sequencing data generated on T and B cells derived from patients with CNS autoimmune disease

  Dataset EGAD00001006232

• Transcriptome Profiling of human AT2 cells in COPD

  RNA-seq of FACS sorted AT2 cells from ex-smokers with (n=6) and without (n=3) COPD at different disease stages. Fastq files are provided.

  Dataset EGAD00001011115

• Methylation Profiling of human AT2 cells in COPD

  WGBS of FACS sorted AT2 cells from ex-smokers with (n=6) and without (n=3) COPD at different disease stages. Fastq files are provided.

  Dataset EGAD00001011116

• Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer

  Dataset consists of 216 samples, with each sample having a BAM, BAI and VCF file.

  Dataset EGAD00001011297

• Whole Exome and Whole Genome Profiling as well Genome-Wide Methylation Profiling from Early to Advanced Chronic Lymphocytic leukemia (CLL), Genome-Wide Methylation Profiling in Monoclonal B Cell Lymphocytosis (MBL)

  Serial whole exome sequencing of samples collected from 21 patients at multiple time points during progression from early to late chronic lymphocytic leukemia (CLL) and one matching non-tumor tissue sample from each patient. Additional whole genome sequencing of samples from 3 selected patients. Genome-wide B cell methylation compared between 5 healthy donors from the same age group as patients, 20 patients with monoclonal B cell lymphocytosis and in serial CLL samples with matching whole exome sequencing. Moreover, genome-wide single-cell RRBS-profiling of B cells from one healthy donor and from one patient with CLL was performed using a protocol newly developed by the A. Meissner group.

  Study phs001431

• Germline Whole-Exome Sequencing of Lung Cancer in EAGLE

  EAGLE is a large population-based case-control study designed and conducted to investigate the genetic and environmental determinants of lung cancer and smoking persistence using an integrative approach that allows combined analysis of genetic, environmental, clinical, and behavioral data. Here, we applied whole exome sequencing (WES) to EAGLE study, in a group of 2,777 Italian subjects (including 1,461 lung cancer cases and 1,316 healthy controls). We derived gene-level burden tests to explore the cumulative effect of deleterious rare variants within protein-coding genes and the lung cancer risk. Additionally, at this site we include WES datasets of 1259 healthy controls from 1054 PLCO (The Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial) subjects and 205 ACS (The American Cancer Society study) subjects.

  Study phs002496

• A study of resistance to novel coronavirus infection in health care workers

  There have been cases of what appear to be nosocomial infections among healthcare workers at several hospitals. The infected healthcare workers were assumed to have contracted the disease through close contact with infected patients. However, we confirmed at each medical institution that there were many healthcare workers who had apparently had closer contact with infected patients than with infected patients, but had not contracted the disease. Thus, the purpose of this study was to clarify the internal factors that make individuals less susceptible to novel coronavirus infection and their stress tolerance, and to establish a system that contributes to the appropriate allocation of healthcare workers and the creation of a system that can more safely deal with this disease in the future.

  Study JGAS000562

• The transcriptomic response of skeletal muscle in life-long high-level trained and untrained men and women after acute exercise

  To investigate the influence of lifelong exercise training on the response of skeletal muscle to a bout of acute exercise we generated global transcriptomic data from long-term endurance (8 men, 8 women) and strength (8 men, 8 women) trained individuals and healthy age-matched untrained controls (8 men, 8 women). Skeletal muscle biopsies were taken from M. vastus lateralis before, directly after, and after 1h and 3hrs following acute exercise. All subjects completed one bout of acute endurance exercise and one bout of acute resistance exercise, separated by 4-8 weeks. All 384 samples were multiplexed in 4 lanes and sequenced (2x250bp paired end) on the Illumina NovaSeq 6000.

  Study EGAS00001006139

• Genomic characterization of hepatocellular carcinoma in Hispanic patients

  The genomic DNA was extracted from paired tumor and adjacent non-tumor samples of 27 Hispanic HCC patients. The TruSeq Rapid Exome Library Prep kit (Illumina, CA) was used to capture the coding regions of the human genome. The 100 bp paired-end sequencing of every 6-plex whole exome library pool was performed on an Illumina HiSeq 3000 system according to the manufacturer’s recommended protocol to achieve an average coverage of ~100X. The paired-end reads were aligned to the human reference genome (hg19) with decoy sequences (as used in the 1000 Genomes Project) using BWA software. The duplicate reads were marked and removed using Picard and SAMtools, respectively. Local realignment around insertions/deletions (indels) and base quality recalibration were performed using GATK.

  Study EGAS00001007431

• RNA sequencing

  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.

  Dataset EGAD00001000285

• med-pchic-dac

  The data are accessible under the terms of the following Data Access Agreement that needs to be filled in, signed (by yourself and your institution’s official contact) and returned by email to med-pchic-dac@lists.cam.ac.uk

  Dac EGAC00001000523

• GBM Up and Down Responder EZH2 ChIPseq

  ChIPseq using anti-EZH2 with a sheared input DNA control to assess EZH2 genomic biding in one longitudinal pair of samples (pre- and post-treatment) from one UP and one DOWN responder GBM patient

  Dataset EGAD50000000134

• Molecular pathways and cellular subsets associated with adverse clinical outcomes in overlapping immune-related myocarditis and myositis

  ScRNA-seq FASTQ files from myocarditis and control cardiac muscle samples; and myositis and control skeletal muscle samples.

  Dataset EGAD50000000488

• FOCUS study

  Shallow whole genome sequencing of adavanced colorectal tumors from patients included in the FOCUS clinical trial. Performed to calculate assocations of irinotecan with copy-number alterations. Copy number aberration analysis of 349 enroled patients.

  Dataset EGAD50000001007

• MS meninges single nuclei RNA sequencing

  10X 3' (RNA) samples of isolated single nuclei from highly inflamed leptomeninges and adjacent grey matter from 3 MS patients used in the paper.

  Dataset EGAD50000001235

• Dataset of Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  This dataset contains genomic profiles of 7 PPM1D-mutated patients across the spectrum of myeloid disorders using single-cell analyses (Tapestri technology) on diagnostic and longitudinal samples.

  Dataset EGAD50000001229

• Whole-exome-sequencing in Frontotemporal dementia (FTD)

  To identify the genetic cause and modifiers of Frontotemporal dementia (FTD), we performed Whole-exome-sequencing of FTD patients.

  Study JGAS000374

• Specific BRCA and immune configurations determine optimal response to platinum-based chemotherapy in triple negative breast and ovarian carcinomas (COH_TNBC_RNAseq)

  To determine the trascriptional profiles of Triple Negative Breast Cancers (COH cohort)

  Study EGAS00001006002

• 16S rDNA amplicon sequencing of 196 human fecal samples of an Inulin cross-over trial

  16S rDNA amplicon sequencing of 196 human fecal samples of an Inulin cross-over trial in healthy, mildly constipated individuals.

  Dataset EGAD00001004956

• TGL49_HBC CHARM panel

  Targeted panel sequencing of hereditary cancer syndrome-associated genes (TP53, BRCA1, BRCA2, PALB2, MLH1, MSH2, MSH6, PMS2, EPCAM, and APC) in plasma and buffy coat samples from healthy control patients.

  Dataset EGAD00001010001

• Whole-genome-seqeuncing IMFT

  Whole-genome sequencing of IMFT tumor samples from 24 participants in the clinical phase II trial EORTC 90101 “CREATE” (CREATE IMFT cohort)

  Dataset EGAD00001007804

• Characterization of a novel MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line WXS

  A novel in-house-made pediatric MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line was characterized

  Dataset EGAD00001009758

• Paired-end Whole Exome-seq analysis of TERT promoter duplication in GBM

  Dataset contains paired-end Whole Exome sequencing data from 5 tumor samples and 1 single normal blood sample from a single primary GBM patient.

  Dataset EGAD00001008768

• Xenograft BC WGS Dataset

  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.

  Dataset EGAD00001001336

• BASIS RNAseq

  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.

  Dataset EGAD00001001264

• RNA-seq of frontal post-mortem human brain tissue

  RNA-sequencing dataset of post-mortem human brain tissue of FTD patients with mutations in GRN, MAPT and C9orf72 and healthy controls.

  Dataset EGAD00001008014

• Dataset of Fastq files of three trio members

  This dataset contains whole genome sequencing data, based in paired end Fastq files of three trio members.

  Dataset EGAD00001008096

• Exome_Sequencing_of_Human_myeloid_malignancies

  This study involves exome sequencing of blood/bone marrow DNA from patients with myeloid malignancies. Blood DNA samples have been taken from patients at different timepoints of disease phenotype. We hope to elucidate mechanisms of clonal evolution in these patients.

  Dataset EGAD00001002213