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• 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

• Ribosomal profiling on Epstein-Barr virus transformed B-lymphoblastoid cell lines

  Epstein-Barr virus-transformed B-lymphoblastoid cell lines from six individuals (HG00114, HG00282, NA12005, NA12044, NA12717 and NA12751) of the GEUVADIS Project were selected for ribosomal profiling. For each EBV-LCL, 20 million cells were treated with 2 μg/ml harringtonine and 100 μg/ml cycloheximide. After lysing cells in lysis buffer supplemented with 100 μg/ml cycloheximide, ribosome complexes were purified by density purification. Small RNA molecules were isolated using the NucleoSpin miRNA Kit (Bioke, Leiden, Netherlands), followed by RNA PAGE gel separation. Universal linkers were added after dephosphorylation. After reverse transcription, the cDNA was circularized and, after ribosomal RNA depletion, barcoded and sequenced on Illumina NextSeq 500.

  Dac EGAC50000000209

• Evaluation of the Efficacy and Safety of a Clinical Grade Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Patch: A Pre-Clinical Study

  Cardiomyocyte-derived induced pluripotent stem cells (iPSCs) may represent a promising therapeutic strategy for severely damaged myocardium. This study aimed to assess the efficacy and safety of clinical grade human iPSC-derived cardiomyocyte (hiPSC-CM) patches and conduct a pre-clinical proof-of-concept analysis.

  Study EGAS50000000188

• RNA-seq from B-ALL patients treated on the ALLG ALL09 study

  Dataset contains RNA-sequencing data (fastq files) from 46 patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL09 study (ACTRN12618001734257). All patients were diagnosed with CD19 positive B-cell acute lymphoblastic leukaemia and were negative for Philadelphia chromosome positive disease. Patient samples (bone marrow or peripheral blood) were taken at diagnosis. mRNA was extracted from lymphoblasts and underwent paired-end sequencing using either the illumina NextSeq (75 bp PE) or MGI DNABSEQ-G400 (100bp PE) platforms. Transcriptomic data was used for identification of genomic drivers of acute lymphoblastic leukaemia (ALL).

  Dataset EGAD50000001603

• Picuris Pueblo Genomic Project – Modern Dataset

  Please refer to the Supplemental Materials of the paper for more information.

  Dataset EGAD50000001245

• 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

• Amplicon–Based Metagenomic Analysis.

  Amplicon-based fungal metagenomic sequencing for the identification of fungal species in brain tissue from Alzheimer's disease. The study consists in 14 samples, sequenced using Illumina's paired-end technology.

  Dataset EGAD00001003196

• 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

• FPKM expression values of the CUP/reference/validation cohort (H021)

  FPKM expression values of the CUP/reference/validation cohort used for tissue-of-origin prediction based on transcriptomic data

  Dataset EGAD00001008638

• Annotated germline variant calls from the lungNENomics project

  Annotated germline variant calls derived from WGS data for 72 individuals from the lungNENomics cohort. Variant calling was performed with Strelka2 and annotation with InterVar.

  Dataset EGAD00001015672

• Genomic gain of EBV's LMP-1 in NKTCL

  The study found a high recurrence of genomic gain of LMP1 locus within EBV-associated NKTCL. The pilot data set and extended dataset of 77 WGS NKTCLs found 18/77 tumoral genomes to harbour genomic gain of LMP-1 locus within the EBV viral genomes within NKTCL tumoral sequencing data. The study also found 1/10 NKTCL cell lines to be positive for LMP-1 locus gain within EBV genomes too. This dataset includes solely the confirmatory WGS data of LMP-1 gain from NKYS cell lines using Oxford Nanopore long-read sequencing technology.

  Study EGAS50000000260

• Single-Cell Transcriptomics of Adult Recurrent Respiratory Papillomatosis

  These single-cell sequencing data were generated from diseased respiratory tract papilloma tissue caused by chronic infection with HPV 6 or 11. Patients from which this tissue was derived participated in a phase I clinical trial using a novel therapeutic vaccine, but these samples were acquired before this experimental treatment. The aim of performing this single-cell sequencing study was to characterize the papilloma cells and other cells in the papilloma microenvironment with single-cell analyses using the 10X Genomics platform. The single-cell gene expression raw data files for each sample will be available in this submission.

  Study phs003349

• The aim of this study was to identify underlying hub genes and dysregulated pathways associated with the development of HCC using bioinformatics analysis.

  In the present study, we identified differentially expressed protein-coding genes from RNA transcriptional profiling performed on 11 paired cancer tissues and adjacent non-cancerous tissues. Then, we conducted GO, KEGG, PPI network and centralities analyses to study and identify changes in pathways and hub genes. The aim of this study was to improve understanding of HCC carcinogenesis by providing information concerning the genetic changes that occur during disease progression and to uncover the expression of biomarkers with potential use for clinical diagnosis, treatment, and monitoring of disease progression.

  Study EGAS00001002526

• T-cell reconstitution after reduced dose ATLG induction in kidney transplant recipients

  Pre-sensitized kidney transplant recipients have a higher risk for rejection following kidney transplantation and therefore receive a lymphodepletional induction therapy with anti human T-lymphocyte globulin (ATLG). The time course of lymphocyte reconstitution with regards to overall and donor-reactive T-cell receptor (TCR) specificity remains elusive. In this study we aimed to describe the TCR repertoire in a reduced dose ATLG regimen making it possible to evaluate shifts in the shape of the immune repertoire and to detect the reappearance of donor-reactive T-cells following reduced lymphodepletional induction therapy.

  Study EGAS00001005941

• Measurement of SARS-CoV-2 variants fraction in infected alveolar cells

  With the continuous emergence of highly transmissible SARS-CoV-2 variants, the comparison of their infectivity has become a critical issue for public health. However, a direct assessment of the viral characteristic has been challenging due to the lack of appropriate experimental models and efficient methods. Here, we conducted full-length transcriptome sequencing of single human alveolar cells infected by multiple SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1). Using unique mutations of each VOC, we calculated the fraction of VOCs in infected cells.

  Study EGAS00001006730

• FASTQ files of the small RNA-Seq dataset from the POPS cohort

  Placental biopsies were collected within 30 minutes of birth and flash frozen in RNAlater(ThermoFisher). For each biopsy,total placental RNA was extracted from approximately 5 mg of tissue using the “mirVana miRNA Isolation Kit” (Ambion) followed by DNase treatment (“DNA-free DNA Removal Kit”, Ambion). RNA quality was assessed with the Agilent Bioanalyzer and all the samples with RIN values ≥ 7.0 were used in the downstream experiments. Total RNA-libraries were prepared from 300-500ng of total placental RNA with the “TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat”(Illumina). Small RNA-libraries were prepared from 150ng of total placental RNA with the “NEBNext Multiplex Small RNA Library Prep Kit for Illumina”(New England Biolabs)and concentrated using the “QIAquick PCR purification kit”(Qiagen). Paired libraries were combined and size selected using the Pippin Prep and 3% Agarose Gel Cassette with marker F (Sage Science),pooled and sequenced (single-end, 50bp) using a Single End V4 cluster kit and HiSeq4000 instrument.

  Dataset EGAD00001004860

• Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions

  Alterations in the DICER1 and DGCR8 microprocessor genes confer risk to the development of benign and malignant thyroid lesions. The involvement of 2 miRNA biogenesis genes in benign and malignant thyroid tumors highlights the key role of miRNAs in the thyroid gland. We traced the progression from benignity to malignancy in DICER1- and DGCR8-mutated thyroid lesions by performing a multiomic characterization of these lesions aiming to uncover unique features characterizing either form for potential use as biomarkers. This multiomic characterization included whole exome sequencing (WES) (N=18), miRNA profiling (N=38), spatial transcriptomics (N=2) and/or methylome (N=281).

  Study EGAS50000001577

• scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment.

  We performed scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment. In order to identify tumor-specific T cells, we selected CD8 T cells that were enriched in the tumor of the patient. We also selected CD8 T cells appearing in the bladder after BCG treatment, with the hypothesis that BCG treatment stimulates tumor-specific CD8 T cells. Next, we cloned the TCR of these T cells in a Jurkat cell line and tested these TCR for recognition of tumor-specific antigens.

  Study EGAS50000001384

• 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

• Genotype data of human CD4 Treg cell

  Genotype data obtained using the coreExome Illumina SNP chip array for all the individuals included in the study of gene expression regulation in human primary regulatory CD4+ T cells (Tregs)

  Dataset EGAD00010001848

• 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

• A study of the immune system in patients with peripheral inflammatory neuropathy (CIDP): RNA adult (2025-10-02)

  Leveraging single-cell sequencing technologies to shed light on the immune aetiology of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) . This dataset contains all the data available for this study on 2025-10-02.

  Dataset EGAD00001015725

• Dataset for "Characterizing the cfDNA fragmentome in patients with hepatocellular carcinoma"

  The dataset includes 63 BAM files from Oxford Nanopore PromethION whole-genome sequencing, generated by base calling POD5 files with Dorado (super-accurate, modified base model v5.0.0_5mCG_5hmCG@v3) and aligning reads to the hg19 reference genome.

  Dataset EGAD00001015823

• NHLBI TOPMed: Children's Health Study (CHS) Integrative Genomics and Environmental Research of Asthma (IGERA)

  The Integrative Genomics and Environmental Research of Asthma (IGERA) Study was proposed to collect immortalized cell lines, RNA, cDNA and DNA from 400 well-characterized subjects who participated in the southern California Children's Health Study (CHS) and to develop an accompanying database for these samples consisting of extensive phenotype, exposure, genome-wide genotype, gene expression, and methylation data. A subset of Hispanic-White participants (n=160) were included in the TOPMed project, including 77 asthma cases and 83 controls.

  Study phs001603

• Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

  The analysis of e2QTL allows for the identification of context-specific eQTL effects (Kim-Hellmuth et al. (2017), PMID: 28814792). To evaluate how inter-individual genetic variability influences the regulation of DNA damage-induced apoptosis, we performed e2QTL analysis of CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.

  Study EGAS50000000666