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• Two scRNA-seq datasets from control and irradiated organoids.

  Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.

  Dataset EGAD50000001933

• Locally advanced prostate cancer cohort

  Fastq files from RNA sequencing and BAM files from tNGS of normal and tumor samples from 17 patients from the locally advanced prostate cancer cohort.

  Dataset EGAD50000002380

• WGS data from 20 cholangiocarcinoma cases

  WGS data from biliary tract cancer samples (Holzapfel, et al., J Gastrointest Oncol,14(1):379-389, 2023). The dataset includes tumour and normal BAM files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=20 tumour/normal pairs).

  Dataset EGAD50000002307

• The Dynamic Immune Behavior of Primary and Metastatic Ovarian Carcinoma

  Single-cell RNA-seq data of prospectively collected normal ovarian tissue sample from 1 healthy individual and tumor tissue samples with or without chemotherapy from 19 HGSOC patients.

  Dataset EGAD50000000057

• Whole Exome Data of RFWD3 Fanconi anemia patient

  Dataset contains one sample derived from gDNA of human fibroblasts. Files are in FASTQ format and were generated using the Agilent SureSelect Human All Exon 50Mb Kit and followed by Next Generation Sequencing on a HighSeq2000 instrument (Illumina).

  Dataset EGAD00001003311

• Transcriptome analysis of Tcells from blood, fat and skin

  Tcells were isolated fom Tissues and FACS sorted. In total 50 samples were processed in 5 replicates with the Takara SmartSeq Stranded kit. Single end fastq-files are supplied.

  Dataset EGAD00001007663

• WXS of IgAN-tGBM, IgAN and TBMN

  The dataset consists of 258 bam files by whole exome sequencing. 122 from IgAN-tGBM patients, 64 from IgAN patients and 72 fromTBMN patients.

  Dataset EGAD00001009287

• mRNA profiling of CAFs and cancer cells in response to TGF-β and BMP signaling

  TGF-β and BMP signalings are important signaling pathways in the tumor microenvironment during cancer progression. This RNA-sequencing (62 fastq pairs) analysis explored how cancer-associated fibroblasts (CAFs) from human (19TT) and mice (Balbc A/B) respond to TGF-β, BMP2, or Gremlin antibody, as well as how cancer cells (66cl4) respond to Gremlin antibodies.

  Dataset EGAD50000001351

• Targeted capture sequencing to identify MYC, BCL2, and BCL6 rearrangements in non-Hodgkin lymphoma

  Targeted capture sequencing of 364 samples representing a mix of Burkitt lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, and high-grade B-cell lymphomas with MYC and BCL2 or BCL6 rearrangements. Capture space covers 3.5 Mb of the human genome including regions around MYC, BCL2, BCL6, PAX5, and IGH/K/L.

  Dataset EGAD50000000489

• Whole exome sequencing and target gene sequencing of ESCC cases and healthy controls from Henan high-risk region

  In total, 186 FH+ ESCC cases were sequenced using whole-exome sequencing, then 1935 ESCC cases and 1186 geographically-matched healthy controls were sequenced using 7 Mb custom designed Roche SeqCap kit which targeted about 600 genes. The libraries were constructed and then sequenced in Illumina platform.

  Dataset EGAD00001004556

• Whole genome sequencing of HSPCs and pAML

  Whole genome sequencing data (Illumina HiSeq and NovaSeq) of clonal cultures derived from pediatric human bone marrow-derived hematopoietic stem and multipotent progenitor cells (in total 44 samples from 10 donors) and bulk pediatric acute myeloid leukemia blasts (in total 6 samples from 6 patients) to study the mutation accumulation.

  Dataset EGAD00001006338

• Summary statistics of meta-analysis using two genome-wide association study of inflammatory bowel disease in Koreans.

  We combined samples from 1,469 inflammatory bowel disease (IBD) patients consisted of 896 Crohn’s disease (CD) and 573 ulcerative colitis (UC) and 4,041 controls used in our previously published GWAS with 1,726 additional IBD patients (725 CD and 1,001 UC) and 378 additional controls genotyped using the Asian Screening Array (ASA). We uploaded summary statistics of three meta-analyses in text files.

  Dataset EGAD00001006983

• Single-cell RNA-seq of patient-derived organoids across three generations

  Single-cell RNA-seq of first-, second-, and third-generation patient-derived organoids. Obtained using the 10X Genomics single-cell 3' expression solution (v3 chemistry). First- and second-generation PDOs from one patient and first-, second-, and third-generation PDOs from three additional patients.

  Dataset EGAD00001008431

• Investigation of chromatin accessibility in clear cell renal cell carcinoma using ATAC-seq

  To identify regions of open and accessible chromatin in clear cell renal cell carcinoma (ccRCC), we performed ATAC-seq on the 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and processed narrowPeak fomats. Data were processed using the nf-core atacseq pipeline.

  Dataset EGAD50000001885

• RNAseq data of polyA+ RNA from Leukocytes from 624 individuals of the ProgeNIA cohort.

  We sequenced the polyA+ fraction of the RNA of the leukocytes from 624 sardinian individuals with RNAseq. Prior to library preparation we added either ERCC ExFold RNA Spike-In. An average of 60M reads per samples with 51 bp paired-end reads were generated on a HiSeq 2000 (Illumina). Sequencing reads were then aligned using STAR-2.2.0c2 to the h37d5 reference genome supplemented with the ERCC spike-ins sequences. We further provided an exon-exon junction database that we generated from the GENCODE v14 annotation. In order to remove a contamination from a parallel experiment, we discarded any reads that mapped to the genomic regions of CBLB (chr3:105370773-105592330) and BCL11A (chr2:60672555-60784156). Filtered aligned reads (bam format) are shared.

  Dataset EGAD00001003102

• Neversmoker lung adenocarcinoma

  Non-small cell lung cancer whole genome sequencing We performed whole genome sequencing of Korean never-smoker lung adenocarcinoma patients to discover novel pathway except EGFR and ALK patients. We identified estrogen signaling as a novel enriched signaling. Lastly we validated the elevated estrogen signaling through immunohistochemistry experiment in some patients which increased signaling.

  Study EGAS50000000232

• 3D genome topology distinguishes molecular subgroups of medulloblastoma

  Medulloblastoma (MB) has four molecular subtypes, but their 3D genome architecture differences are unclear. We used in situ Hi-C on 28 surgical specimens and a patient-derived xenograft to reconstruct the 3D genome architecture of MB subtypes, finding that topologically associating domain (TAD) insulation scores could distinguish MB subtypes.

  Study EGAS50000000540

• Pediatric B-cell precursor acute lymphoblastic leukemia samples with very early relapse

  In this study we performed a genomic analysis of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations. In addition, we included one case with a good initial treatment response and on-treatment relapse at the end of upfront therapy.

  Study EGAS00001005615

• Genome and transcriptome sequence data from a colorectal adenocarcinoma patient (Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer)

  Genome and transcriptome sequence data from a colorectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study. These data are included in the manuscript entitled, "Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer".

  Dataset EGAD00001001876

• TK-EPN862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - RNAseq

  In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. RNAseq data (paired end) provided here correspond to Primary tumour, two metastatic lesions (one spinal, one cranial), and a patient-derived xenograft derived from the patient.

  Dataset EGAD00001009870

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (Owen)

  Study EGAS00001005855

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Edinburgh, Scotland, UK.

  Study EGAS00001005843

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (O'Donovan)

  Study EGAS00001005852

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Landen, Stockholm, Sweden.

  Study EGAS00001005838

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Stockholm, Sweden (Pedersen)

  Study EGAS00001005856

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of three hyperdiploid ALL patients (ALLT-329, ALLT-347, ALLT-356). Sequencing libraries were made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using Illumina HiSeq X.

  Dataset EGAD50000002425

• RNA sequencing of intestinal metaplasia

  We perform bulk RNA-seq of 10 and single cell RNAseq of 2 intestinal metaplasia samples. We also perform stereoseq spatial transcriptomic analysis of 4 gastric cancer samples. The dataset contain cram files from 10 bulk RNAseq samples, and raw fastq files from 2 single cell RNAseq and 4 stereo-seq samples.

  Dataset EGAD50000002010

• WGS data of paediatric ETV6::RUNX1 B cell acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and CRAM files from second relapse and matched remission (control) samples of one ETV6::RUNX1 ALL patient (ALLK-104). Sequencing libraries were made using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both second relapse (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002286

• Single-cell whole-genome sequencing dataset of sorted CD3+, CD33+, and CD34+ cells from aplastic anemia

  This dataset contains raw single-cell whole-genome sequencing data generated from a single patient with aplastic anemia using the BioSkryb platform. Single cells were isolated based on surface marker expression (CD3+, CD33+, and CD34+) and subjected to whole-genome amplification followed by sequencing on an Illumina platform.

  Dataset EGAD50000002195

• Sequencing data for oesophageal and related samples - BOs release 5 (RNA)

  Dataset EGAD00001005385

• Sequence Data for Paper: Epigenetic reprogramming during differentiation of human CD4+ T lymphocytes into memory stages

  Sequence Data of total RNA, miRNA, WGB, mRNA, NOMe, Chip (H3K27ac,H3K27me, H3K36me3, H3K4me1, H3K4me3, H3K9me3, Input) Short Desrciption: Epigenetic profiling of human CD4+ memory T cells reveals their proliferative history and argues in favor of a progressive differentiation model driven by epigenetically controlled master regulators.

  Dataset EGAD00001001865

• Genomic data of acute myeloid leukemia cases for integration with metabolomic analyses

  Whole exome sequencing (WES) data of paired (germline and leukemic) samples of 100 adult patients affected by acute myeloid leukemia. Targeted sequencing data of myeloid-related genes of 21 leukemia (not paired) samples from adult patients affected by acute myeloid leukemia.

  Dataset EGAD00001007941

• WGS data from both single-cell and bulk samples

  This dataset contains the raw BAM/CRAM files used in the manuscript "Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma" Steemers et al. (2026). This includes: - 332 PTA-based single-cell WGS samples (~15X depth) - 7 bulk tumour samples (~30X depth) with matched germline samples (~30X depth) - 14 bulk tumour samples seqeunced by the Princess Maxima Centre diagnostics department (~105X depth) with matched germline samples (~35X depth)

  Dataset EGAD50000002411

• RNASeq profiles from Indian HFrEF Cohort

  The dataset contains whole transcriptomics profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Total transcriptome libraries were prepared using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold kit and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001196

• Whole Genome DNA Methylation MPI

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Catalog No. 30024), the EZ DNA Methylation-Gold Kit (Zymo, D5005) and DNA Clean & Concentrator-5 (Zymo, D4013), following the instruction manual Accel-NGS® Methyl-Seq DNA Library (Revision 160510). Paired-end libraries (2 × 150 bp) were sequenced on a NovaSeq 6000 instrument.

  Dataset EGAD50000001139

• Whole Genome DNA Methylation

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences 30024), the EZ DNA Methylation-Gold Kit (Zymo D5005), and DNA Clean & Concentrator-5 (Zymo D4013), following the instruction manual Accel-NGS Methyl-Seq DNA Library (Revision 160510). Paired-end (2 x 150 bp) libraries were sequenced on a DNBSEQ-T7 instrument (MGI) after library conversion.

  Dataset EGAD50000000766

• Reproducibility of variant calls in replicate next generation sequencing experiments

  To examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA, we performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. This data set contains 17 breast cancer samples that were sequenced in duplicate (n=14) or triplicate (n=3), in order to assess concordance of all calls and single nucleotide variant (SNV) calls.

  Dataset EGAD00001001209

• Leiden_melanomafamilies

  Around 10% of patients who present in melanoma clinics have a first degree relative with a previous diagnosis of melanoma. While around 3% have three or more relatives who have been diagnosed with the disease. In this project we will whole genome sequence patients from large Dutch familial melanoma pedigrees to identify mutations in genes that drive melanomagenesis. The identification of these genes will facilitate the management of familial melanoma patients and their families.

  Dataset EGAD00001002186

• low pass WGS of patient from the CN300 cohort

  We copy number profiled 688 tumor regions from 300 patients presenting with advanced prostate cancer and prospectively followed-up (median, 7 years) in the control group of the STAMPEDE trial. Patients were categorised into four metastatic states, namely high-risk non-metastatic (with or without local lymph node involvement) or metastatic (low or high volume).

  Dataset EGAD00001008800

• Targeted analysis of chondrosarcoma cancer genes (2019-04-01)

  Targeted analysis of chondrosarcoma cancer genes . This dataset contains all the data available for this study on 2019-04-01.

  Dataset EGAD00001004877

• WGS data subfolder HFF7VCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HFF7VCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001007075

• 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

• 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

• CALGB/SWOG 80405 ct DNA Biomarker Evaluation

  To investigate treatment-specific mutations that underlie resistance to treatment with chemotherapy +/- bevacizumab or cetuximab in first line metastatic Colorectal Cancer (mCRC) patients, we performed targeted sequencing of circulating free DNA (cfDNA) from longitudinal plasma samples. These samples were collected at baseline (PRE, n=354), during treatment (OTH, n=254), and/or at progression or end of the protocol treatment (EOT, n=345) from CALGB/SWOG 80405, a randomized phase III trial that evaluated the efficacy of chemotherapy plus bevacizumab or cetuximab treatment in first line colorectal cancer patients (NCT00265850).

  Study phs002941

• NIBIT-EPI-MESO study samples

  Multi-omics analysis of pre-immuno checkpoint inhibitors (ICI) therapy lesions from 91 pleural mesothelioma (PM) patients enrolled in the multicenter NIBIT-EPI-MESO study. Neoplastic lesions were characterized using multiple molecular platforms, including RNA sequencing (n=82), Whole Exome Sequencing (WES) (n=87), Reduced Representation Bisulfite Sequencing (RRBS) (n=83) and cell-free methylated immunoprecipitation sequencing (cfMeDIP-seq) (n=18). Tumor samples were collected during the standard diagnostic pleuroscopy or thoracoscopy before ICI therapy. Matched Peripheral Blood Mononuclear Cells (PBMC) were collected from PM patients before ICI therapy.

  Study EGAS50000001478

• Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility

  Effect of biallelic variants in genes of the piRNA pathway on biogenesis of pachytene piRNAs. RNA isolated from snap frozen testicular tissue

  Study EGAS50000000397

• ctDNA detectability and representativeness in seven body liquids from female patients with metastatic breast cancer - lpWGS

  low-pass Whole Genome Sequencing (lpWGS) to assess the representativeness of seven body liquids from female patients with metastatic breast cancer.

  Study EGAS50000001302

• ctDNA detectability and representativeness in seven body liquids from female patients with metastatic breast cancer - WES

  Whole Exome Sequencing (WES) to explore the mutational status of seven body liquids from female patients with metastatic breast cancer.

  Study EGAS50000001303

• eSENSES control samples

  This dataset comprises BAM files from 18 control samples analyzed with the eSENSES targeted NGS panel. Spanning approximately 2 Mb, the panel features around 15,000 evenly distributed genome-wide SNPs, over 500 focal SNPs targeting key breast cancer driver regions, and more than 2,000 exons from 81 commonly altered genes.

  Dataset EGAD50000001167

• Whole exome DNA sequencing data of pretreatment tumor biopsies and matched blood samples of patients treated in the OpACIN-neo trial

  The dataset includes whole exome DNA sequencing on pre-treatment tumor biopsies of lymph node metastases (n=60) matched with blood samples (n=60)

  Dataset EGAD00001006730