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• 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.

  Dataset EGAD00001008663

• Single-cell RNA-seq of peripheral blood mononuclear cells in classic Hodgkin lymphoma

  Abstract: Classic Hodgkin lymphoma (cHL) is a largely MHC class I-negative tumor with recurrent 9p24.1/ PD-L1/ PD-L2 copy gains and the highest reported response rates to PD-1 blockade. We utilized scRNA sequencing to characterize the peripheral immune response to PD-1 blockade and more broadly define non-CD8+ dependent mechanisms of immune evasion in cHL. Peripheral blood mononuclear cells were obtained from 20 patients with relapsed/refractory (R/R) cHL treated with PD-1 blockade (nivolumab) on the CheckMate 205 clinical trial (paired samples from cycle 1 day 1 [C1D1] and cycle 4 day 1 [C4D1]), 11 patients with newly diagnosed, previously untreated cHL and 13 healthy donors.

  Dataset EGAD00001011360

• HLA has strongest association with IgA nephropathy in genome-wide analysis

  GWAS study of families with probands with IgA nephropathy from the UK Glomerulonephritis DNA bank

  Study EGAS00000000031

• The sanger result of LAM disease

  Tumor biopsies from LAM disease were analyzed by sanger to characterize the alterations in patients ,to elucidate the landscape of genetic/genomic alterations. The dataset include 21 samples.

  Dataset EGAD00010001761

• Single cell PDAC samples

  h5 files from 15 single cell PDAC samples described in "Transcription phenotypes of pancreatic cancer are driven by genomic events events during tumour evolution"

  Dataset EGAD00010001811

• HSP90 inhibitor resistant cells

  K562 cells were treated with different HSP90 inhibitors (PuH71 and Coumermycin A1) and the CNV profil was compared to the parental K562 (untreated). In addition, the CNV profile of HSP90AB1 knockout K562 cells was analyzed.

  Dataset EGAD00010002336

• Structural variants

  Structural variants assessed in 6 patient samples with varying phenotypes, through the use of sniffles2 with a support parameter of 1 and at a length of 30 bp

  Dataset EGAD50000000741

• Contribution of specific cell types to the development of Barrett’s esophagus and carcinoma via germline genetic risk

  We sought to elucidate how individual cell types in Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) contribute to disease development via germline genetic risk.

  Dac EGAC50000000235

• COVID-19 progression and convalescence in common variable immunodeficiency patients

  Longitudinal analysis of single-cell RNAseq datasets of PBMCs from COVID-19 CVID patients and controls.

  Study EGAS50000000368

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• Investigating Delayed-Onset Drug Hypersensitivity Reactions Prospectively

  Delayed-type drug hypersensitivity reactions (dtDHR) are significant causes of morbidity and mortality, but the origin, phenotype and function of pathogenic T cells across the spectrum of severity are unknown. Research has been hampered by several barriers. We leveraged recent technical advancements to study skin-resident memory T cells (TRM) versus recruited T cell subsets in the pathogenesis of severe systemic forms of disease, Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) and drug reaction with eosinophilia and systemic symptoms (DRESS), and skin-limited disease, morbilliform drug eruption (MDE). As part of the overarching study, we used single cell RNA sequencing (scRNA-seq) with CITE sequencing and TCR sequencing on prospectively collected skin and blood samples from patients with SJS/TEN and MDE patients. We compared this to healthy controls obtained from discarded skin from surgeries and discarded blood collars from a blood donation center. These data are included here in dbGaP database. The overarching study also performed bulk transcriptional profiling and microscopic analysis of clinical skin samples, as well as a mouse model of MDE (PMID: 39042477). Together, the data supported clonal expansion and recruitment of cytotoxic CD8+ T cells (identified using the mean normalized expression of NKG7, GNLY, GZMA, GZMB, and PRF1) from circulation into skin, along with both expanded and non-expanded cytotoxic CD8+ skin TRM in SJS/TEN whereas MDE displayed a cytotoxic T cell profile without expansion or recruitment of cytotoxic CD8+ T cells from circulation implicating TRM as the potential cause of disease. Concurrently, MDE displayed a pro-Treg signature, highlighted by CCR8 and TNFRSF4 (OX40), which promotes Treg survival compared to SJS/TEN.

  Study phs003344

• Inherited chromosomally-integrated human herpesvirus 6A/B (HHV-6A/B) genome sequences in the Japanese population

  The deposited sequences represent inherited chromosomally-integrated human herpesvirus 6 (iciHHV-6) genomes identified from 10 BioBank Japan (BBJ) subjects based on the analysis of the whole-genome sequencing (WGS) data. In brief, we re-aligned unmapped reads from the WGS to HHV-6A genome (Genbank accession number: KJ123690.1) using BWA-MEM algorithm. Ten out of 3,256 subjects were identified with high depth of coverage of HHV-6. We further distinguished subjects with integrated HHV-6A subtypes from those with integrated HHV-6B based on phylogenetic analysis of concatenated sequences of three viral genes (U27/U43/U83, which show high divergence between viral species). We reconstructed the HHV-6 viral genome of 10 subjects. First, reads that mapped to a reference HHV-6A genome (KJ123690.1) were further aligned against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM. Based on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8 {Garrison, 2012}. We generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7. Please note that HHV-6B-specific variants are unlikely to be sensitively reconstructed using this method.

  Study JGAS000240

• Identification of ALS Associated Genes Using Whole Genome Sequencing

  The overall aim of this study is to discover of novel genetic elements associated with amyotrophic lateral sclerosis (ALS). Towards this goal, we have performed exome and whole genome sequencing for over 2000 samples. This data will be process and harmonized to yield high quality variant calling. These variants will be combined with control cohorts to identify novel genetic elements associated with ALS through case: control analyses.

  Study phs001585

• Acral melanoma targeted exome sequencing study (UCSF)

  Acral melanoma affects world populations irrespective of skin color. It has comparatively few single nucleotide mutations, but exhibits genomic instability characterized by structural rearrangements and amplifications. As acral melanoma harbors BRAF (GeneID:673) mutations at low frequencies, we searched for alternative therapeutic targets. We performed targeted deep sequencing of cancer-related genes on 37 acral melanomas and identified point mutations, structural rearrangements and copy number alterations.

  Study phs001596

• Clinical and Genetic Analysis of Retinopathy of Prematurity (ROP)

  Retinopathy of prematurity (ROP) is a leading cause of childhood blindness worldwide and is treated based on the presence of symptoms of "plus disease", a dilation and tortuosity of retinal vessels. This project aims to identify the genetic and clinical underpinnings of the disease by comparing the germline variants of ~1,400 premature babies. 100 samples have been selected for WES and all have been genotyped.

  Study phs002047

• Shotgun metagenome sequencing of saliva samples using PromethION

  Using PromethION, we conduct shotgun metagenome sequencing of human saliva, where both bacteria and bacteriophages are densely living, to study both microbiome and virome. We aim to explore, for example, relative abundance of bacteira and bacteriophages, distribution of contig lengh. types of phages and prophages, frequency of novel phages revealed by the long-reads and their taxonomic classification, and characteristics of genes encoded by the phages.

  Study JGAS000186

• Genotype data from Nagahama cohort project

  Genotype data with basic phenotypes (age and gender) for 3693 samples from Nagahama Cohort project are provided. Genotyping are performed by A)Human610-Quad?B)HumanOmni2.5-4?C)HumanOmni2.5-8?D)HumanOmni2.5S?E)HumanCoreExome?F)HumanExome BeadChip from Illumina Inc. 1708, 1017, 185, 112, 479 and 192 samples are genotyped by A only, B only, C only, A+B+E, B+D+F and C+D+F respectively.

  Study JGAS000012

• Whole exome sequencing data of tumor/normal pairs for the study "TGF-β attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells"

  Tumor DNA was extracted from formalin-fixed and paraffin embedded tumors of a large cohort of bladder cancer patients before treatment with anti-PD-L1. Normal DNA was extracted from matched PBMCs. Whole exome sequencing was performed. This is a subset of patients for which RNA sequencing is also provided (with more detailed phenotypic information).

  Dataset EGAD00001004218

• RNA_expression_profiling_of_melanoma_patient_derived_xenograft

  Patient-derived xenografts (n=96) were derived from metastatic melanoma patients. RNA expression profiling will be preformed to study 1. HLA-typing and 2. the effect of the tumour microenvironment on tumour growthThis 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/

  Study EGAS00001001537

• ATAC_SEQ_MAIN___PHASE_1

  This is a study to test ATAC-seq protocols. CD4+ and CD8+ cells have been obtained from three different anatomical compartments. We aim to assay open-chromatin regions across these cells and perform comparative analyses.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/

  Study EGAS00001000947

• Mutation_analysis_in_human_iPS_cells_

  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 by 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/

  Study EGAS00001000359

• Gut metagenome/FINRISK 2002 (Salosensaari et al. Nature Comms 2021)

  The main goal of the project is the study the associations between the gut metagenome and human health. The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012).

  Study EGAS00001005020

• Shallow whole genome sequencing and targeted capture sequencing data of PCNSL and PTL primary and relapse pairs

  Shallow whole genome sequencing for copy number analysis and targeted capture sequencing data for translocation and mutation anslysis of paired primary and relapse PCNSL and PTL samples

  Dataset EGAD00001008387

• Single cell transcriptomes of of primary tumors and normal endometrial derived organoids treated with DBZ

  Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed single cell sequencing on endometrial and ovarian tumours, and on organoids both treated with DBZ and normal and found both secretory-like and ciliated-like tumour cells.

  Dataset EGAD00001006280

• COVID-19 Multiomics Atlas

  We provide a single-nuclei RNA-sequencing (snRNA-seq) dataset derived from four COVID-19 patients, generated using the 10x Chromium Next GEM Single Cell v3.1 kit. For our study, these were integrated with snRNA-seq data with 12 publicly available sc/snRNA-seq datasets, comprising organ donor lung samples (n=89) and COVID-19 lung tissue samples (n=51). Additionally, we provide a spatial transcriptomic dataset characterizing different histopathological stages of diffuse alveolar damage, across a cohort of 33 COVID-19 patients. This was generated using the Nanostring Whole Transcriptome Assay (WTA) with regions of interest (ROIs) sized 400 µm² each. This integrated multi-omics analysis of snRNA-seq, histology, and spatial transcriptomics data, is available for exploration and download via our web portal: https://covid19-multiomicatlas.cellgeni.sanger.ac.uk/.

  Dataset EGAD00001015404