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• plasma dna fragmentations

  Data were generated by next-generation sequencing (Illumina) in a fastq format. This dataset involved sequencing data from pregnant women and patients with hepatocellular carcinoma (HCC). For HCC samples, the paired buffy coat and tumor DNA tissue samples were also sequenced.

  Dataset EGAD00001006054

• Gut microbiota in prediabetes and diabetes

  Here, we profiled the gut microbiota in a discovery (n = 1,011) and validation (n = 484) cohort comprising Swedish subjects naive for diabetes treatment and grouped by glycemic status.

  Dataset EGAD00001006351

• Mutation analysis using a custom SureSelect panel

  All baseline samples and when available EOT were processed for high-resolution mutation analysis. We designed a SureSelectXT-HS custom panel (Agilent) covering 68 genes with a total size of 260kb using the Agilent SureDesign platform.

  Dataset EGAD00001006386

• Fibromyalgia versus small fiber neuropathy: Diverse keratinocyte transcriptome signature dataset

  We provide a diverse keratinocyte transcriptome signature between SFN and FMS patients, which may hint towards distinct pathomechanisms of small fiber sensitization and lay the basis for advanced diagnostics in both entities

  Dataset EGAD00001006918

• RNA sequencing data pre-treatment and post-treatment for NABUCCO cohort 1

  NABUCCO cohort 1 sequencing data. The dataset includes RNA sequencing pre-treatment on tumor samples (n=18) and RNA sequencing post-treatment on bladder tumor samples (n=18).

  Dataset EGAD00001006855

• WCDT deep RNA-seq

  This dataset includes fastq files for total RNAseq of 104 patient biopsies with metastatic castration resistant prostate cancer. The RNAseq libraries were rRNA depleted and sequenced at 150bp paired-end on Illumina Novaseq.

  Dataset EGAD00001008799

• CBD-KEY-RNASEQ-GENOTYPES: Genotype SNP data

  gVCF file per patient obtained from the bulk/mini-bulk RNAseq data. For further information regarding this dataset, please contact Stephen Sansom and Alexander Mentzer at contact@combat.ox.ac.uk.

  Dataset EGAD00001007959

• Persistent Mutation Burden Drives Sustained Anti-Tumor Immune Responses.

  Data includes whole exome sequenced bam files for matched tumor-normal pairs from the study.

  Dataset EGAD00001009697

• Treatment arm information and sample sheet

  Table of treatment arm information for the 418 RNAseq evaluable population.

  Dataset EGAD00001009502

• Genomic and transcriptomic determinants of host susceptibility, protection, and viral mutation in experimental SARS CoV-2 infection: RNA (2025-08-11)

  Single-cell profiling of healthy adult volunteers that were inoculated with SARS-CoV-2. . This dataset contains all the data available for this study on 2025-08-11.

  Dataset EGAD00001015679

• Dataset for ARHGAP11A knockout and control organoid cells.

  This dataset contains 9 RNA sequencing samples of hiPSC-derived forebrain organoid ARHGAP11A knockout and hiPSC-derived forebrain organoid control cells. Sequencing was performed on Illumina NovaSeq 6000. The sequencing was always paired.

  Dataset EGAD00001015706

• Dataset for ChIP and Transcriptomic sequencing of neuroblastoma tumor samples(hipo)

  This dataset contains ChIP and Transcriptomic sequencing of 32cneuroblastoma tumor samples. The sequencing was performed on Illumina HiSeq 2000 and Illumina HiSeq 4000 respectively.

  Dataset EGAD00001015808

• Additional RNAseq data of metastatic breast cancer samples

  Paired-end RNA sequencing data from 33 metastatic breast cancer samples. Sequencing was performed on the Illumina NovSeq 6000 using NEBNext Single Cell and Low Input RNA Library Prep Kit for Illumina.

  Dataset EGAD00001015678

• Decade-Long Leukemia Remissions with Persistence of CD4+ CAR T-Cells

  Two patients with chronic lymphocytic leukemia (CLL) were treated with CD19 targeted CAR T therapy and followed over several years. Peripheral blood from both patients at multiple time points was collected, and 5' CITE-Seq with TCR profiling was performed on sorted CD3+CAR+ T cells at multiple time points. Here, we deposit the raw sequencing data for these single-cell experiments. Processed and de-identified data (e.g. cellranger output, Seurat objects) have been made available on a separate public data repository.

  Study phs002931

• High-Throughput and High-Dimensional Single Cell Analysis of Antigen-Specific CD8+ T Cells

  We developed a high-dimensional, tetramer associated T cell receptor sequencing (TetTCR-SeqHD) method to simultaneously profile cognate antigen specificities, TCR sequences, targeted gene-expression, and surface protein expression. Cultured antigen-specific CD8+ T cell clones were studied as a proof-of-concept experiment. In addition, both the antigen specific CD8+ T cells from healthy subjects and Type I diabetic patients were investigated. 18 individually consented subjects pooled into four groups for sample processing

  Study phs002441

• Modulation of Lung Immune Responses to Viral Infection-Microbiome Interactions with Respiratory Organoids

  Here, we colonized bronchial epithelial air-liquid interface tissue cultures with 58 different individual microbes. Following 18 and 48 hours of colonization, we performed bulk RNA-seq of the host epithelial cells (n=3). Overall, we found significant microbial species-level and strain-level variation in host gene expression changes for innate immunity and epithelial barrier genes. Of particular interest, we found significant heterogeneity in stimulation of host interferon and antiviral interferon-stimulated genes.Study registered in ImmPort under accession # SDY2281.

  Study phs003627

• ATACseq of primary fibroblasts and iPSC-derived endoderm cells in CPRF patients with LSD1 mutations and healthy controls

  Primary fibroblasts or iPSC-derived endoderm cells from two CPRF patients carrying distinct heterozygous point mutations in histone demethylase LSD1/KDM1A and their healthy fathers were expanded and split into two cell culture wells and independently passaged twice before cell collection. Nuclei were isolated from the two biological replicates of each individual-derived fibroblasts and used for bulk ATAC-seq library preparation. Libraries were sequenced in paired-end mode on Illumina NextSeq 500. 

  Study EGAS00001008238

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  SARS-CoV2 mRNA vaccination-induced CD4+ Th cells were isolated based on activation marker expression from human bone marrow (n=3), lung (n=5), liver (n=4) and paired blood samples (to liver donors, n=4) of virus-naive vaccinees after Spike peptide mix stimulation in vitro. The 10X platform was used for single cell transcriptome analysis, along with T cell receptor clonotype analysis in a total of 1985 cells. Samples were sequenced on a NovaSeq 6000 (Illumina).

  Study EGAS50000000045

• Patient tumour data (RNAseq, WGBS, ChIPseq, WGS)

  Content: 60 GB patient tumours and 4 normal brain samples combined in pairs by region (x2=8 total input samples). RNAseq: 1 lane per sample, total strand-specific rRNA-depleted (normal samples were combined = 2 lanes/samples per brain region). WGBS: 2 lanes per sample (normal samples were combined = 2 lanes/samples per brain region). ChIPseq (histone mark): a subset of 20 GB samples were profiled. For the same modification were multiplexed and sequenced on 4 lanes each (H3K27ac, H3K4me1) or a single lane (all others). WGS: used as matching input control for the 20 ChIPseq samples. Data type and technology: RNA-seq: PE 100bp sequenced on HiSeq2000. WGBS: PE 100bp sequenced on HiSeq2000/4000. ChIPseq: SE 50bp sequenced on HiSeq2000/4000. WGS: PE 150bp sequenced on HiSeq X.

  Dataset EGAD00001005492

• CCA RNA-seq data (60 CCA, 6 normal, 16 cell-line)

  Fastq files for RNA-seq for 60 CCAs, 6 normal bile duct tissues, 14 CCA cell-lines (including replicates), and 2 normal cholangiocyte cell-lines (including replicates). RNA was extracted using the Qiagen RNeasy Mini kit. Illumina Tru-Seq Stranded Total RNA kit (Illumina, San Diego, California, USA) was used to prepare RNA libraries from 1 µg of total RNA. Paired-end 150 bp sequencing was performed using Illumina HiSeq4000 sequencer with the paired-end 150 bp read option.

  Dataset EGAD00001011998

• BLUEPRINT ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001000326

• Benchmark Dataset for Somatic Mutation Calling in Cell-Free DNA

  This study provides a comprehensive benchmarking resource for somatic variant detection in cell-free DNA (cfDNA) from cancer patients. Longitudinal plasma samples from colorectal and breast cancer cohorts were selected to create patient-matched dilution series spanning ultra-low to high circulating-tumour-DNA (ctDNA) fractions, while preserving each individual’s germline and clonal haematopoiesis background. Deep whole-genome sequencing (150×) and ultra-deep whole-exome sequencing (2,000×) generated a reference call set of ~37,000 single-nucleotide variants and ~58,000 insertions/deletions. These data enabled systematic evaluation of nine somatic variant callers across variable ctDNA levels and sequencing depths, and were further used to explore machine-learning–guided parameter tuning. The resulting dataset offers an openly accessible framework for developers and clinicians to assess and optimize somatic variant calling in liquid biopsy applications.

  Dataset EGAD50000001870

• Variant calls for "Quality of Whole Genome Sequencing from Blood versus Saliva Derived DNA in Cardiac Patients"

  Paired blood and saliva samples from five unrelated individuals were directly compared for quality of whole genome sequencing. Two (Sample Pairs 1 and 2) were female probands diagnosed with tetralogy of Fallot, a type of congenital heart disease, and three (Sample Pairs 3, 4 and 5) were male probands diagnosed with hypertrophic cardiomyopathy. WGS was performed using Illumina HiSeq X to a target average coverage depth of 30x and a read length of 150 bp. The resulting reads were not filtered for minimum quality in order to avoid losing possible contaminant reads. Sequencing read alignment was done using Isaac Aligner to human genome build hg19. Short variant i.e. single-nucleotide variant (SNV) and small insertion-deletion (indel) calling was performed using Isaac Variant Caller with default parameters.

  Dataset EGAD00001005772

• The Celiac Gene Expression Data Access Committee

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Dac EGAC50000000630

• mRNA-seq data from ALL patients with NUP214::ABL1 disease

  Dataset contains mRNA-sequencing data (fastq files) from 2 patients with NUP214::ABL1 disease (one T-ALL and one B-ALL patient). Patient samples (peripheral blood or bone marrow) were taken at diagnosis (B-ALL) or relapse (T-ALL). mRNA was extracted from lymphoblasts and underwent paired-end sequencing (75bp) using the Illumina NextSeq platform. Transcriptomic data was used for identification of gene fusions, SNVs and InDels. mRNA-seq data for an additional B-ALL patient with NUP214::ABL1 disease utilised in this study has already been published (EGAS00001006460).

  Dataset EGAD50000001395