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• Immune cell atlas of environmental and ancestral diversity in Indonesia [scRNAseq]

  Island Southeast Asia (ISEA) remains consistently underrepresented in large-scale human genomic resources despite its rich ancestral and lifestyle diversity. The region's complex population history and environmental/pathogen pressures could have shaped its populations' unique immune responses. Here, we generated single-cell PBMC profiles from 199 Indonesians sampled across four populations in the islands of Bali and New Guinea. The dataset consists of low-pass whole genome sequencing and pooled single-cell PBMC transcriptome sequencing. These groups capture diversity in regional genetic ancestries (West ISEA-like and Papuan-like) and lifestyle contrasts (urban versus rural communities in Bali; highland versus lowland communities in New Guinea), providing a window into how ancestry and environment jointly shape immune variation across ISEA. Together, this study provides the first large-scale single-cell immune atlas of ISEA, highlighting how ancestral and environmental diversity jointly shape human immunity in this globally important yet understudied region.

  Study EGAS50000001656

• Immune cell atlas of environmental and ancestral diversity in Indonesia [WGS]

  Island Southeast Asia (ISEA) remains consistently underrepresented in large-scale human genomic resources despite its rich ancestral and lifestyle diversity. The region's complex population history and environmental/pathogen pressures could have shaped its populations' unique immune responses. Here, we generated single-cell PBMC profiles from 199 Indonesians sampled across four populations in the islands of Bali and New Guinea. The dataset consists of low-pass whole genome sequencing and pooled single-cell PBMC transcriptome sequencing, including T-cell receptor (TCR). These groups capture diversity in regional genetic ancestries (West ISEA-like and Papuan-like) and lifestyle contrasts (urban versus rural communities in Bali; highland versus lowland communities in New Guinea), providing a window into how ancestry and environment jointly shape immune variation across ISEA. Together, this study provides the first large-scale single-cell immune atlas of ISEA, highlighting how ancestral and environmental diversity jointly shape human immunity in this globally important yet understudied region.

  Study EGAS50000001655

• ATAC-seq of iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimicking MPNST progression

  ATAC-seq data used in the paper "iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities" by Uriarte-Arrazola, 2026. The uploaded data was used to explore and validate the cellular model as an MPNST progression model.

  Study EGAS50000001764

• WGS of iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimicking MPNST progression

  WGS data used in the paper "iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities" by Uriarte-Arrazola, 2026. The uploaded data was used to explore and validate the cellular model as an MPNST progression model.

  Study EGAS50000001765

• RNA-seq of iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimicking MPNST progression

  RNA-seq data used in the paper "iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities" by Uriarte-Arrazola, 2026. The uploaded data was used to explore and validate the cellular model as an MPNST progression model.

  Study EGAS50000001766

• Single-cell TCR sequencing of gluten-specific T cells from 20 celiac disease patients uploaded on 2021

  To examine the T-cell receptors of the gluten-specific T cells in celiac disease, we isolated single CD4+ T cells from blood , gut biopsies or T-cell lines generated from gut biopsies using HLA-DQ2.5 tetramers and determined the sequences of rearranged TCRalpha and TCRbeta gene pairs.

  Study EGAS00001005047

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

  This dataset includes combined single-cell RNA-Seq and T cell receptor profiling data for SARS-CoV-2 spike protein-reactive CD4+ T cells and NK cells from blood, liver, lungs, and bone marrow of human donors.

  Dataset EGAD50000000062

• WGS and WTS data for manuscript titled: Pathologist-initiated whole genome and transcriptome sequencing demonstrates diagnostic utility in resolving difficult-to-diagnose tumors

  Illumina platform sequencing of whole genome libraries prepared from normal and cancer samples and whole transcriptome libraries from cancer samples from 45 donors

  Dataset EGAD00001015615

• scRNASeq of human innate lymphoid cells from different compartments

  Group 1 innate lymphoid cells (ILCs) comprise a heterogeneous family of cytotoxic natural killer (NK) cells and ILC1s. We identifiy a population of “liver-type” ILC1s with transcriptional, phenotypic, and functional features distinct from those of conventional and liver-resident NK cells as well as from other previously described human ILC1 subsets. LT-ILC1s were CD49a+CD94+CD200R1+, expressed the transcription factor T-BET, do not express the activating receptor NKp80, or the transcription factor EOMES. Similar to NK cells, liver-type ILC1s produce IFN-γ, TNF-α, and GM-CSF; however, liver-type ILC1s also produce IL-2 and lack perforin and granzyme B. Liver- type ILC1s are expanded in cirrhotic liver tissues, and they can be produced from blood-derived ILC precursors in vitro in the presence of TGF-β1 and liver sinusoidal endothelial cells. Cells with similar signature and function can also be found in tonsil and intestinal tissues. Collectively, our study identifies and classifies a population of human cross-tissue ILC1s.

  Study EGAS00001006847

• RNA-seq of iPSC-derived microglia treated with miRNA mimics and inhibitors

  Microglia were derived from iPSCs and treated with mimics and inhibitors of the miRNAs hsa-miR-150-5p, hsa-miR-193a-3p and hsa-miR-19b-3p. RNA-sequencing was then performed to examine the effects of up- and down-regulation of the respective miRNAs.

  Dataset EGAD00001006842

• Archive growth Statistics

  EGA Statistics Bibliography Growth Community Archive Distribution Catalogue In this section, we expose the overall volume of data available to download and the different archived file types. EGA Archive growth in size and number of files The below figure represents the EGA archive growth in size (TB) and number of files. EGA Archive Growth per year lineChart('ega-archive-growth', 'https://stats.ega-archive.org/growth/archive', ['Volume (TB)'], ['T']) Archive files The below figure represents on a initial level, the percentage of archived files by data technology. The second level, acessible by clicking in the required extension, displays the number of files by extension archived in the ega archive. Please click over the extension to learn more about the files. EGA Archived Files barChart('ega-archived-files', 'https://stats.ega-archive.org/extensions', false ,'', true)

  Documentation about/statistics/archive

• WES data for genomic determinants of response and resistance to inotuzumab in B-ALL

  Whole exome sequencing data for 69 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000097

• Exome sequencing for paired tumor/normal samples from patients with corticotropin-independnet Cushing's syndrome

  Exome sequencing was performed for paired tumor/normal samples from patients with corticotropin-independnet Cushing's syndrome. Tumor DNA was extracted from adrenocortical adenomas and normal DNA was extracted from adjacent adrenal tissues or periphral blood.

  Dataset EGAD00001000715

• WGS files for Klco-NUP98 data

  WGS files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015443

• WXS files for Klco-NUP98 data

  WXS files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015444

• RNASeq files for Klco-NUP98 data

  RNASeq files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015445

• scRNASeq files for Klco-NUP98 data

  scRNASeq files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015479

• ChIPseq data for Glioblastoma (EGAS00001003953, H016)

  ChIPseq data for human glioblastoma patients, EGAS00001003953. Mix of input, H3K27ac, H3K27me1, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3 and BRD, 20 human samples, 2 cell lines (LN229, ZH487).

  Dataset EGAD00001006548

• High-throughput sequencing data for study of molecular drivers of resistance to castration in localised prostate cancer

  Aligned whole-genome sequencing and RNA-seq of localised prostate cancer for study 'Loss of SNAI2 in prostate cancer correlates with clinical response to androgen deprivation therapy'.

  Dataset EGAD00001006640

• CBD-RAW-REPERTOIRE-T: T cell bulk repertoire sequence files

  fastq and filtered fasta files for T-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007961

• Latency and interval therapy affect the evolution in metastatic colorectal cancer

  The cohort of 15 patients included ten patients with available tissue from the primary tumor and ≥1 metastatic site, four patients with pairs of metastases only, and one patient with an anastomotic recurrence five years after initial resection of the primary tumor

  Dataset EGAD00001005226

• Genomic and transcriptomic profiling of colorectal cancer patient-derived organoids

  This study describes controlled-access human sequencing data generated from colorectal cancer patient-derived organoids established using the CTOS method. Whole-exome sequencing (WES) and RNA sequencing (RNA-seq) were performed to characterize genomic alterations and transcriptomic profiles of the organoids.

  Study EGAS50000001669

• Innate immune cell subsets are enriched in synovial fluid of ACPA-negative rheumatoid arthritis and characterised by distinct type I IFN gene signatures

  This study provides a detailed comparison of the myeloid cell landscape in the SF of patients with ACPA+ and ACPA− RA, highlighting the unique involvement of type I IFN responses in ACPA− RA.

  Study EGAS50000001260

• Whole Exome Sequencing of Bipolar cases, matched controls at Broad Inst on a cohort from Netherlands

  This research project was a collaboration between VU and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 943 Bipolar case/control samples from collaborators in the Netherlands. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and the samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000619

• Uterine leiomyoma: DNA methylation, chromatin activity and gene expression

  In this study, we observed the effects of different uterine leiomyoma driver mutations to tumor DNA methylation, chromatin activity and gene expression, to form a comprehensive view on the epigenetic consequences of the mutations.

  Study EGAS00001004499