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• Single-cell RNA and TCR sequencing of 16 PSCC and 6 non-malignant samples

  We included 16 fresh tumor samples of biopsy-proven invasive penile squamous cell carcinomas and 6 adult non-malignant inner prepuce samples. Single-cell RNA sequencing was performed (10x genomics). An HPV reference genome of 15 high-risk HPV types was generated and we mapped all single cell reads to the GRCh38 human and HPV reference genome using CellRanger. Targeted next-generation sequencing (tNGS) was performed for the detection of TP53 loss-of-function mutations.

  Dataset EGAD50000000317

• Transcriptomic changes in placenta associated with anesthesia, delivery mode and maternal diabetes

  Samples were from 34 mothers, 6 with gestational diabetes, 14 with type 1 diabetes and 14 without diabetes history with either vaginal (N=17) or cesarean section (n=17) delivery, comprising primary planned section (N=9) or secondary emergency section (N=8). Anesthesia methods during delivery included spinal (N=11), epidural (N=11), or local anesthesia (N=6), with unknown anesthesia information for six cases. Samples from each other were from the Villous and the Decidua part of the Placenta

  Dataset EGAD50000000701

• Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays

  - WES files from primary or metastatic prostate cancer biopsies, from patients with metastatic prostate cancer. - This dataset includes those cases profiled by WES and included in the manuscript Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays, Arce-Gallego et al, Cell Rep Med 2024 - The dataset includes WES for 80 tumor biopsies from 65 different patients, including paired tumor/normal samples.

  Dataset EGAD50000001018

• Whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing data from nasal cells of COVID-19 patients

  Nasal swabs were collected from COVID-19 patients during the acute phase of infection as well as 3 and 12-months post-infection. Cells isolated from nasal swabs were subjected to whole-genome enzymatic DNA methylation sequencing (n=33) and scRNA-seq (n=24). For n=12 former COVID-19 pateints, follow-up samples were collected at 3 and 12 months post-infection and subjected to scRNA-seq.

  Dataset EGAD50000000398

• AWI-Gen Phase 1 GWAS Genotype data

  The samples were genotyped on the H3Africa array (~2.3M SNPs) using the Illumina FastTrack Sequencing Service2. The default Illumina pipeline was used for the genotype calling (build GRCh37/hg19). The data was converted to PLINK using the h3abionet/h3agwas/call2plink pipeline and QC done using the h3abionet/h3agwas/qc pipeline

  Dataset EGAD00010001996

• Exploration of predictive biomarkers for postoperative recurrence of stage II/III colorectal cancer using genomic sequencing

  To identify biomarkers that can predict treatment outcomes, we compared the mutational profiles of surgically resected specimens from patients with recurrent cancer with those from patients with non-recurrent cancer. Target sequencing, whole-exome sequencing (WES), or whole-genome sequencing (WGS) was perfomed.

  Study JGAS000335

• Chemotherapy accelerates genomic aging of normal blood in children treated for cancer

  Whole genome sequencing (WGS) data obtained from clonally expanded hematopoietic stem and progenitor cells (HSPCs) from pediatric cancer patients before and after therapy exposure. In addition, WGS data of cord-blood derived HSPCs clones exposed to various chemotherapeutics and radiation was obtained.

  Study EGAS00001005141

• WGS data subfolder HFFWLCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HFFWLCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008495

• Somatic mutation and clonal evolution in the human bladder_WES (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-exome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006115

• Somatic mutation and clonal evolution in the human bladder Novaseq (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-genome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006116

• Human lung cell atlas 10x and SS2 sequencing data (3 of 3)

  Contains FASTQs for cells from 20 10x channels across 2 NovaSeq runs, 42 384-well plates across 6 NovaSeq runs, and 12 96-well plates across 4 NextSeq runs.

  Dataset EGAD00001006128

• Whole-genome sequencing of rhabdomyosarcoma tumouroids (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumoroids data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015707

• Sequencing data for oesophageal and related samples - Scott et al (WGS, RNA)

  Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files

  Dataset EGAD00001006738

• Whole Exome and RNA-Sequencing of Germline, Small Bowel Carcinoid Primary Tumor, and Liver Metastasis Trios

  This dataset includes trios of germline/constitutional, primary tumor (small bowel carcinoid), and metastatic tumor (liver) trios for 5 patients (i.e. 15 samples total). Constitutional, primary tumor, and metastatic tumor samples all underwent whole exome sequencing (WES or WXS). Primary and metastatic tumor samples underwent RNA sequencing (RNA-seq).

  Dataset EGAD00001010036

• mRNA-Seq on single human MII oocytes collected from gonadotropin stimulated women

  This dataset contains 11 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from gonadotropin stimulated women undergoing fertility treatments. M-II stage oocytes were collected and flash frozen prior to lysis followed by RNA extraction, full length cDNA preparation and amplification using the Ultra-low-input SMART-Seq2 v4 kit from Takara Clonetech. Further, these cDNA were used to prepare libraries for sequencing according the Nextera XT DNA library preparation kit from Illumina.

  Dataset EGAD00001006863

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (WGS)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. WGS (BAM files) 5 Barrett's samples 5 normal oesophageal samples 5 normal gastric cardia samples 5 normal duodenal samples

  Dataset EGAD00001006874

• Anthropological dataset 1 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_SampleInfo_FINAL_01062022.txt" Column 1 corresponds to individual alphanumeric codes as in the "eGAdeposit_233CaboVerde_GenotypeFile_FINAL_01062022.vcf" genotype file Column 2 corresponds to individual's biological sex as per genetic inference Column 3 corresponds to individual's self-reported age in years Column 4 corresponds to individual's self-reported cumulated number of years spent in academic or professional education

  Dataset EGAD00001008976

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015714

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015718

• H3Africa Consortium WGS VCF

  Joint called VCF for whole genome sequence data from 410 samples described in the paper: PMID:33116287. It includes 314 high coverage (average 30X) samples sequenced on the Illumina X-Ten, also available as individual datasets under the H3Africa Chip study (EGAS00001002976) and 112 medium coverage (average 10X) samples from the TrypanGen study (EGAS00001002602) sequenced on Illumina HiSeq 2500. Supplementary table 3 of the paper describes the geographic breakdown of the samples. 16 samples from the Southern African Human Genome project have been removed from this VCF.

  Dataset EGAD00001008577

• Dataset for Ewing_sarcoma_PNET-RNA

  Rare cancer sequencing data of 28 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008845

• Sequencing data for oesophageal and related samples - Black et al (WGS)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS OACs/BOs/normals)

  Dataset EGAD00001011187

• WGS data subfolder HF3NYCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HF3NYCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008494

• Sequencing data for oesophageal and related samples - OACs 496 release (WGS)

  Data from 496 OCCAMS (Oesophageal Cancer Clinical And Molecular Stratification) cases. WGS BAM files 496x oesophageal adenocarcinoma samples 496x normal samples

  Dataset EGAD00001007785

• Human lung cell atlas 10x and SS2 sequencing data (1 of 3)

  Contains FASTQs for cells from 20 10x channels across 2 NovaSeq runs, 42 384-well plates across 6 NovaSeq runs, and 12 96-well plates across 4 NextSeq runs.

  Dataset EGAD00001006126