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• Sequencing data for oesophageal and related samples - OACs release 1 (RNA)

  Dataset EGAD00001002259

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - barretts_1

  Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357

  Dataset EGAD00001001394

• Single Cell RNA sequencing of Organoids from TSC2+/- patient IPSCs in H- and L-medium

  This dataset contains single cell RNA sequencing data from Organoids grown in high nutrient (H) and low nutrient (L) medium. Organoids were grown for 110 days. Organoids were grown from a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) and an isogenic control cell line (TSC2+/+).

  Dataset EGAD00001006332

• scTCR-seq from brain metastasis micorenvironment and cerebrospinal fluid

  A total of 9 brain metastasis were sequenced. For 6/9 a matched cerebrospinal fluid sample, prior to surgery and in two cases after surgery (+1 month from surgery) and after treatment (+3 month) were collected. Single-cell T cell receptor clonotypes were produced using the Chromium Single Cell 5’ Library and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD00001006451

• scRNA-seq from brain metastasis micorenvironment and cerebrospinal fluid

  A total of 9 brain metastasis were sequenced. For 6/9 a matched cerebrospinal fluid sample, prior to surgery and in two cases after surgery (+1 month from surgery) and after treatment (+3 month) were collected. Single-cell gene expression was produced using the Chromium Single Cell 5’ Library and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD00001006452

• RNAseq before and after cold pressor test

  The cold pressor test (CPT) is a widely used pain provocation test to investigate both pain tolerance and cardiovascular responses. Twenty-two females were phenotypically assessed before and after a CPT, and blood samples were taken for RNA-sequencing. Files were processed and quantified with kallisto v0.42.5 using the human reference transcriptome (Gencode Release 28). Countdata was rlog-transformed.

  Dataset EGAD00001009649

• Telomere attrition becomes an instrument for clonal selection in aging hematopoiesis and leukemogenesis

  Whole genome sequencing of 288 single-cell-derived blood colonies from 3 individuals with splicing factor-mutated clonal hematopoiesis.

  Dataset EGAD00001015640

• MILK-Omics: Systems Biology of Human Milk and Its Links to Maternal and Infant Health

  The primary objective of the project is to generate a systems-level view of human milk in the context of healthy mothers and their term infants. The study uses biospecimens and clinical data from the Mothers and Infants LinKed for Healthy Growth Study (MILk Study), a prospective observational cohort of approximately 500 exclusively breastfeeding women and their infants who are followed to 6 months of age. The project focuses on mature milk samples collected at 1 month postpartum and infant gut microbiome samples collected at 1 and 6 months of age. Specific Aim 1 is to identify maternal genetic and clinical factors that shape human milk gene expression. Using bulk and single-cell RNA sequencing of the milk cell pellet and genotypes from maternal DNA, we will identify novel genetic determinants of the milk transcriptome and assess potential modification of these genetic associations by gestational weight gain, diet, and other clinical factors. Specific Aim 2 is to describe key features of the normative human milk biosystem and their interactions with one another. Specifically, machine learning techniques will be used to characterize interaction networks and correlational structures among the following features of human milk: transcriptomics, microbiomes, oligosaccharides, metabolomics, lipidomics, and milk macronutrient composition. Specific Aim 3 is to establish how the milk biosystem is related to variation in infant gut microbiomes and health. dbGaP will house the maternal genotype and milk transcriptomics data.The infant microbiome sequence data are associated with BioProject PRJNA1019702.

  Study phs003408

• Phase I Study of the Oral PI3kinase Inhibitor BKM120 or BYL719 and the Oral PARP Inhibitor Olaparib in Patients with Recurrent Triple Negative Breast Cancer or High Grade Serous Ovarian Cancer

  We analyzed massive parallel sequence data from patients with breast and ovarian cancer and identified single base substitution mutational signature 3 (Sig3) - extracted using SigMA - as a biomarker of homologous recombination deficiency (HRD) and predictive for response to PARP inhibitors. Participants were patients enrolled in clinical trials as 2 independent datasets: (1) high-grade serous ovarian cancer and triple-negative breast cancer (TNBC) from a Phase 1b trial of the PARP inhibitor olaparib in combination with the PI3K inhibitor buparlisib (BKM120) (NCT01623349), and (2) TNBC patients who received neoadjuvant olaparib in the Phase II PETREMAC trial (NCT02624973).

  Study phs003019

• Targeting EGFR in NF1 Mutant Melanoma

  Our study focused on melanoma patients with driver mutations in the neurofibromin 1 (NF1) tumor suppressor gene, a subset of melanoma patients that have not benefitted from recent treatment advances. We have leveraged patient-derived short-term cultures (STCs) and multiomics approaches to identify molecular features that could be developed into therapies for NF1 mutant melanoma patients. Our studies revealed that the epidermal growth factor receptor (EGFR) is highly expressed and active in NF1 mutant melanoma cells, and that genetic or pharmacological EGFR inhibition impaired tumor cell proliferation, survival, and cell growth in patient-derived NF1 mutant but not NF1 wild-type melanoma models.

  Study phs003906

• Spatial and temporal genomic evolution in glioblastoma

  Tumor heterogeneity is a challenging barrier to successful targeted therapy in glioblastoma. Identifying the mechanisms that drive cancer cells as they genetically evolve and adapt in response to treatment is a vital goal of modern cancer research. Analysis of sequencing data provides a method for uncovering the mechanisms sustaining tumor heterogeneity and driving evolution. Here, we analyzed genomic profiles of GBM biopsies taken from pre- and post-treatment GBMs (with matched germline controls), to understand 1) the intratumoral clonal compositions of primary GBM and 2) how GBM responds to therapeutic intervention. Our results provide a molecular portrait of GBM recurrence.

  Study EGAS00001001033

• The landscape of somatic mutation in normal colorectal epithelial cells

  The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic events and consequent clonal expansions leading to cancer. As for most cancer types, however, understanding of the earliest phases of colorectal neoplastic change, which may occur in morphologically normal tissue, is comparatively limited because of the difficulty of detecting somatic mutations in normal cells. Each colorectal crypt is a small clone of cells derived from a single recently-existing stem cell. Here, we sequenced hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed, some ubiquitous and continuous, others only found in some individuals, in some crypts or during some phases of the cell lineage from zygote to adult cell. Likely driver mutations were present in ~1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium.

  Dataset EGAD00001004192

• Isala Citizen Science Project: Cross-sectional branch

  The Isala Citizen Science Project, is named after the first female doctor in Belgium, Isala Van Diest (1842-1916). In a co-creative way, volunteers provided samples and data, proposed research objectives and survey questions, and helped to disseminate and interpret the objectives and results through different media platforms, jointly breaking taboos on women’s and vaginal health. In Flow 1, we collected a single sample from a cross-section of the population, characterized the microbiome, and associated it with data collected in questionnaires. Here, we provide extensive sample meta-data for over 3000 women who completed questionnaires on their lifestyle, diet, health, contraceptive use and environment.

  Study EGAS00001006934

• Raw multi-omics dataset from the lungNENomics cohort of lung neuroendocrine tumours

  This study contains raw multi-omics data generated as part of the lungNENomics project, a multi-omics study aimed at deep molecular profiling of lung neuroendocrine tumours, including typical carcinoids (grade 1) and atypical carcinoids (grade 2). The study includes whole-genome sequencing (WGS), RNA sequencing (RNA-seq), and Infinium MethylationEPIC array data from samples in the lungNENomics cohort. These raw data complement the associated processed molecular data released on Zenodo (10.5281/zenodo.19366762) and the corresponding whole-slide pathology images deposited in the EBI BioImage Archive (10.6019/S-BIAD3143). See Sexton-Oates et al medrxiv 2025 (https://www.medrxiv.org/content/10.1101/2025.07.18.25331556v1) for details.

  Study EGAS00001005979

• Genomic landscape of malignant peripheral nerve sheath tumor (MPNST)

  Neurofibromatosis type 1 (NF1) is the most common tumor predisposition syndrome, and is associated with an aggressive soft-tissue sarcoma, malignant peripheral nerve sheath tumours (MPNSTs), the greatest cause of morbidity and mortality in people with NF1. The only potentially curative therapy involves surgery which is not always possible. Even therapy with curative intent is associated with poor overall survival for both sporadic and NF1-related MPNSTs. The development of novel therapies has been largely hindered by a lack of understanding of the molecular events underpinning MPNST pathogenesis. This is a comprehensive multi-omic study of MPNST evolution based on whole genome sequencing and transcriptomic data.

  Study EGAS00001006069

• Single Cell Genome Sequence for DLP+ library A118782A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050B passage 1, patient-derived xenograft SA1050E passage 1 on DLP+ library A118782A

  Dataset EGAD00001009435

• Functional Multiomics of Cellular Therapy and Immune Checkpoint Blockade Therapy for Solid Tumors

  Tumor samples were collected from a patient with synovial sarcoma, which acquired resistance to ACT targeting NY-ESO-1. Biopsies (n=3; primary, metastasis, and recurrence) were subjected to bulk tumor DNA and RNA sequencing, as well as high-dimensional spatial profiling of RNA and protein targets. Bulk tumor whole exome and RNA sequencing corresponding to all three tumor specimens and whole exome sequencing from patient-matched normal blood are made available through this accession.

  Study phs002762

• Cas9-targeted-based long-read sequencing for genetic screening of RPE65 locus

  In order to compare sequencing performance of different technologies in a specific locus, we sequenced blood samples of five inherited retinal dystrophies (IRD) patients harboring a monoallelic variant in RPE65 that remained uncharacterized with: 1) Clinical exome targeted sequencing (CES), 2) whole genome sequencing (WGS), and 3) Long-read sequencing on a MinION platform where CRISPR-Cas9 guide RNA probes were designed to target a 31 kb region including the entire RPE65 locus.

  Study EGAS50000000596

• RNA-seq study of longitudinal blood cell samples drawn from children at risk of type 1 diabetes

  The appearance of type 1 diabetes (T1D)-associated autoantibodies is the first and only measurable parameter to predict progression toward T1D in genetically susceptible individuals. However, autoantibodies indicate an active autoimmune reaction, wherein the immune tolerance is already broken. Therefore, there is a clear and urgent need for new biomarkers that predict the onset of the autoimmune reaction preceding auto-antibody positivity or reflect progressive b-cell destruction. Here we report the mRNA sequencing-based analysis of 306 samples including fractionated samples of CD4+ and CD8+ T cells as well as CD4, CD8 cell fractions and unfractionated PBMC samples longitudinally collected from seven children who developed beta-cell autoimmunity (case subjects) at a young age and matched control subjects.

  Dataset EGAD00001005767

• Full blood mRNA sequencing of myotonic dystrophy type 1 patients after cognitive behavioural therapy

  This dataset consists of 60 mRNA sequencing runs from full blood of 31 myotonic dystrophy type 1 patients, of which for 27 patients reliable data is available before and after 10 months of cognitive behavioural therapy. >30 million 150 bp paired end reads were obtained with UMI-labeled adapters to facilitate filtering of PCR duplicates. Via UMI-analysis we found samples with the aliases sample_01 and sample_02 to contain a very high number of PCR duplicates and recommend the use of these samples only with highest caution or not at all.

  Dataset EGAD00001008383

• Anthropological dataset 2 for The admixture histories of Cabo Verde

  Datasets used in the article "The genetic and linguistic admixture histories of the islands of Cabo Verde" by Laurent R et al. eLife 2023 (DOI: https://doi.org/10.7554/eLife.79827 - URL: https://elifesciences.org/articles/79827) File name "eGAdeposit_233CaboVerde_GEOcoordFULL_FINAL_01062022.txt" Column 1 corresponds to individual alphanumeric codes as in the "eGAdeposit_233CaboVerde_GenotypeFile_FINAL_01062022.vcf" genotype file Column 2-3 corresponds to X-Y GPS coordinates of individual's interview location in Cabo Verde Column 4-5 corresponds to X-Y GPS coordinates of individual's self-reported residence location at the time of the interview Column 6-7 corresponds to X-Y GPS coordinates of individual's self-reported birth-place location Column 8-9 corresponds to X-Y GPS coordinates of individual's self-reported paternal birth-place location Column 10-11 corresponds to X-Y GPS coordinates of individual's self-reported maternal birth-place location

  Dataset EGAD00001008977

• Tubulointerstitial fibrosis is the histological hallmark of chronic kidney disease (CKD). Hypoxia and inflammation (i.e., interleukin (IL)-1β signalling) are independent mediators of tubulointerstitial fibrosis. However, the physiological response of human kidney tubular cells to IL-1β/IL-1RI signalling under the hypoxic conditions of CKD is poorly understood and remains a clinical imperative for therapeutic targeting. This study reports that hypoxia and IL-1β act in synergy to trigger cell cycle arrest/cellular senescence of ex vivo patient-derived primary proximal tubular epithelial cells (PTECs).

  Hypoxia and interleukin (IL)-1β are independent mediators of tubulointerstitial fibrosis, the histological hallmark of chronic kidney disease (CKD). Here, we examine how hypoxia and IL-1β act in synergy to augment maladaptive proximal tubular epithelial cell (PTEC) repair in human CKD. Ex vivo patient-derived PTECs were cultured under normoxic (21% O2) or hypoxic (1% O2) conditions in the absence or presence of IL-1β and examined for maladaptive repair signatures. Hypoxic PTECs incubated with IL-1β displayed a discrete transcriptomic profile distinct from PTECs cultured under hypoxia alone, IL-1β alone or under normoxia. Hypoxia+IL-1β-treated PTECs had 692 ‘unique’ differentially expressed genes (DEGs) compared to normoxic PTECs, with ‘cell cycle’ the most significantly enriched KEGG pathway based on ‘unique’ down-regulated DEGs (including CCNA2, CCNB1 and CCNB2). Hypoxia+IL-1β-treated PTECs displayed signatures of cellular senescence, with reduced proliferation, G2/M cell cycle arrest, elevated senescence-associated β-galactosidase (SA-β-gal) activity and increased production of pro-inflammatory/fibrotic senescence-associated secretory phenotype (SASP) factors compared to normoxic conditions. Treatment of Hypoxia+IL-1β-treated PTECs with either a senolytic drug combination, quercetin+dasatinib, or a type I IL-1 receptor (IL-1RI) neutralizing antibody attenuated senescent cell burden. Our data identify a mechanism whereby hypoxia in combination with IL-1β/IL-1RI signalling trigger PTEC senescence, providing novel therapeutic and diagnostic check-points for restoring tubular regeneration in human CKD.

  Study EGAS00001007904

• Whole genome sequence: cardiomyopathy, 1 myotonic dystrophy patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000706

• scRNA dataset for 15 samples

  This dataset includes single cell (sc)RNA-seq of N=3 patient-derived xenograft (PDX) samples profiled at baseline (no drug treatment) and N=12 samples from one PDX profiled during the course of treatment (N=1 sample each for 4 treatment arms x 3 timepoints). The dataset includes bam files that have been purged of reads mapping to cells where a majority of the reads from that cell mapped to the mouse genome. All scRNA-seq data were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) from 10X Genomics.

  Dataset EGAD50000001424

• SUM-seq data for Macrophage polarisation to M1 and M2 phenotypes experiment

  We stimulated iPSC-derived M0 macrophages with LPS and IFN-γ to induce M1 polarization or IL-4 to induce M2 polarization. To discern early and sustained responses at chromatin accessibility and gene expression levels, we collected samples at five time points along the two polarization trajectories; prior to stimulation (M0) and at 1-hour, 6-hour, 10-hour, and 24-hour intervals, each sampled in duplicates totaling 18 samples, and subjected them to SUM-seq library preparation. Sequenced files for both data modalities are provided as demultiplexed fastq files.

  Dataset EGAD50000001206