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• RNASeq files for Roussel MBPRP

  RNASeq files for Roussel paper titled "Combination of CDK4/6 with BET-bromodomain and PI3K/mTOR inhibitors in medulloblastoma in vitro and in vivo"

  Dataset EGAD00001008842

• WGBS data for ependymomas and normal controls (fetal and adult)

  Whole genome bisulfite sequencing data for 6 ependymomas plus 3 fetal controls (f1, f2, f4) and 3 adult controls (a2, a3, a4). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).

  Dataset EGAD00001000966

• Paired-end Whole Exome-seq analysis of GBM, additional patient.

  Dataset contains one paired-end Whole Exome sequencing sample. One normal blood sample is also included.

  Dataset EGAD00001011989

• Piloting exome resequencing in consanguineous families with homozygosity mapping intervals

  This pilot study aims to generate pilot data to inform future study designs in consanguineous families or inbred populations by resequencing the exome of six individuals from five families with neurodevelopmental diseases. For all of these families a single mapping interval containing the causal variant has previously been identified.

  Study EGAS00001000024

• Data from Shea et al Can Research 2025

  This dataset contains single cell RNA sequencing (192 fastq files for 59 samples), whole exome sequencing (20 BAM files -hg38- for 20 samples) and bulk RNA sequencing (138 paired-end fastq files and 17 single-end fastq files for 8 samples)

  Dataset EGAD50000001334

• RNA seq of intestinal biopsies and blood cells from patients with celiac disease and controls

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Study EGAS50000001104

• Breast implant-associated anaplastic large cell lymphoma shallow whole genome sequencing for copy number analysis and Whole exome sequencing data.

  Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) shallow whole genome sequencing of 29 BIA-ALCL patients for copy number analysis and 24 Alk-negative ALCL samples as control cohort. 7 Whole exome sequencing BIA-ALCL samples.

  Study EGAS00001003962

• Contribution of Retrotransposition to Developmental Disorders

  Variants and WGS data for Gardner et al. 2018 (biorxiv 471375). One VCF each for Alu, L1, and SVA. Flat text file and WGS for processed pseudogenes.

  Dataset EGAD00001004586

• NGS data of human NES cells and tumors

  Raw RNA-seq data for WT and 2 Gorlin NES cells, tumors derived from MYCN mis-expressed WT NES cells, tumors derived from Gorlin NES cells, and tumors derived from Gorlin NES cells transduced with mutant DDX3X (R351W and R534S) and CRISPR/Cas9 targeting GSE1 (each sample has 3 replicates/tumors except Gorlin NES cell tumors have 4). Raw whole exome sequencing data for WT and Gorlin 1 NES cells, tumors derived from MYCN mis-expressed WT NES cells, and tumors derived from Gorlin NES cells (each sample has 3 replicates/tumors except Gorlin NES cell tumors have 4). Raw data for amplicon sequencing of GSE1 and KDM3B at regions targeted by CRISPR/Cas9 in Gorlin NES cells.

  Dataset EGAD00001004990

• Whole-exome sequencing of Fanconi anemia-like inherited bone marrow failure syndrome

  We identified three fibroblast cultures derived from aplastic anemia patients in the Japanese Cancer Research Resources Bank (JCRB) Cell Bank that showed high levels of sister chromatid exchanges (SCEs) in PHA-stimulated lymphoblasts. To elucidate the genetic basis of the high SCE, we carried out whole exome sequencing of these samples. Subsequently, germline variants were analysed for these patients.

  Study EGAS00001003809

• ITER-FIISC Data Access Committee

  DAC for whole-genome variant calling data of individuals from the study of allergic diseases in the Canary Islands.

  Dac EGAC50000000180

• Dataset for 9 samples from the study EGAS00001007891

  This dataset links 9 samples from the study "Phosphoproteomics adds value to treatment recommendations in molecular tumor boards" (EGAS00001007891) to the study EGAS00001007934. Further information about the samples can be found in the respective studies.

  Dataset EGAD50000002316

• Response labels from NABUCCO cohort 1 (NCT03387761)

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes the Response labels used for the analysis of the data. Details about the clinical definitions of Response can be found on the paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006853

• Massachusetts General Hospital Cancer Center DAC for high-throughput microfluidic enrichment from whole leukopak for CTC-based liquid biopsy

  Whole genome sequencing and whole exome sequencing data of circulating tumor cells isolated from patients with metastatic prostate cancer and liver cancer.

  Dac EGAC50000000423

• Array data for oesophageal and related samples – Ganguli et al (methylation array)

  Array data for oesophageal and related samples – Ganguli et al (methylation array)

  Dataset EGAD00010002682

• RNASeq files for Newman MAP3K8 melanoma

  RNASeq files for MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004567

• Severe acne GWAS meta-analysis

  Summary statistics of a GWAS meta-analysis for severe acne. A total of 7,441,713 genotyped and imputed variants were used for 5,602 European severe acne cases and 21,120 matched population controls.

  Dataset EGAD00001004419

• Sequencing data for Murtaza et al. Nature Communications 2015 (doi:10.1038/ncomms9760)

  Exome and targeted amplicon sequencing data for tumor, germline and plasma samples from a patient with metastatic breast cancer.

  Dataset EGAD00001002108

• Whole exome sequencing study for 8 pairs of primary NSCLCs and distant metastases

  Whole exome sequencing study for 8 pairs of primary NSCLCs and distant metastases. This dataset includes a total of 30 samples.

  Dataset EGAD00001005764

• Additional RNASeq files for Roussel MBPRP

  Additional RNASeq files for Roussel paper titled "Combination of CDK4/6 with BET-bromodomain and PI3K/mTOR inhibitors in medulloblastoma in vitro and in vivo"

  Dataset EGAD00001009394

• Single cell RNA sequencing of colorectal cancer patients (KUL3)

  All libraries were sequenced on Illumina HiSeq4000 until sufficient saturation was reached.

  Dataset EGAD00001008584

• Cancer RNA-seq consisting of FASTQ single-end reads from colon cancer sample

  Cancer RNA-seq consisting of FASTQ single-end reads from 1 colon-cancer individual RNA-seq was performed on illumina This dataset contains reads from a single region.

  Dataset EGAD00001007949

• Characterization of a novel MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line RNA-Seq

  A novel in-house-made pediatric MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line was characterized

  Dataset EGAD00001009759

• Single cell RNA sequencing of lung adenocarcinoma.

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes.

  Study EGAS00001003681

• SNP data for Ovarian cancer PRS (controls)

  SNP data of 28 sites required for the Ovarian cancer PRS (controls)

  Dataset EGAD00001008145

• KiCS cancer panel data for academic and for-profit use

  This data set contains KiCS cancer panel data for academic and for-profit use.

  Dataset EGAD00001009734

• DAC for the study EGAS00001003572

  Dac EGAC00001001174

• RCIDIBAPS001

  DAC created by the Research Computing platform of IDIBAPS for the submission of 2 WES (Whole exome sequencing) samples provided by Sergi Castellví-Bel

  Dac EGAC50000000466

• ITER-FIISC Data Access Committee (FPF)

  DAC for Whole-exome variant calling of individuals from the study of familial pulmonary fibrosis in the Canary Islands.

  Dac EGAC50000000473

• Roifman DAC

  This Data Access Committee will oversee all requests for data submitted by Dr. Chaim Roifman at the Hospital for Sick Children in Toronto, Canada. Requests should be directed by email to chaim.roifman@sickkids.ca.

  Dac EGAC50000000396

• RNASeq files for Mullighan ECOG2993 data

  RNASeq files for paper titled "Molecular classification improves risk assessment in adult B-lineage ALL: Patients on the international UKALLXII-ECOG2993 trial."

  Dataset EGAD00001006380

• Thymic epithelial transplantation for complete DiGeorge syndrome Spatial (2025-07-28)

  Spatial transcriptomics study of thymic transplant biopsies . This dataset contains all the data available for this study on 2025-07-28.

  Dataset EGAD00001015659

• Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells

  Resolving causal genes for type 2 diabetes at loci implicated by genome-wide association studies (GWAS) requires integrating functional genomic data from relevant cell types. Chromatin features in endocrine cells of the pancreatic islet are particularly informative and recent studies leveraging chromosome conformation capture (3C) with Hi-C based methods have elucidated regulatory mechanisms in human islets. However, these genome-wide approaches are less sensitive and afford lower resolution than methods that target specific loci. Methods: To gauge the extent to which targeted 3C further resolves chromatin-mediated regulatory mechanisms at GWAS loci, we generated interaction profiles at 23 loci using next-generation (NG) capture-C in a human beta cell model (EndoC-βH1) and contrasted these maps with Hi-C maps in EndoC-βH1 cells and human islets and a promoter capture Hi-C map in human islets. Results: We found improvements in assay sensitivity of up to 33-fold and resolved ~3.6X more chromatin interactions. At a subset of 18 loci with 25 co-localised GWAS and eQTL signals, NG Capture-C interactions implicated effector transcripts at five additional genetic signals relative to promoter capture Hi-C through physical contact with gene promoters. Conclusions: High resolution chromatin interaction profiles at selectively targeted loci can complement genome- and promoter-wide maps.

  Dataset EGAD50000000517

• PDAC organoids treated with LGK974

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of LGK974 treated pancreatic ductal adenocarcinoma (PDAC) organoids from three different patients for 24h

  Study EGAS50000001542

• Bulk and single-cell AML RNA-seq post ex vivo culture

  Bulk and single-cell RNA-seq performed on primary AML blasts cultured ex vivo for 3 days in standard or niche-like conditions.

  Study EGAS00001006265

• TSG knock-out in hiPSCs (2017-08-10)

  We will perform RNAseq to evaluate the effects of the loss of a list of TSGs on the transcriptome. This dataset contains all the data available for this study on 2017-08-10.

  Dataset EGAD00001003556

• Assessing gene expression profiling from FFPE Patient Samples: A Comparison of Two Library Preparation Approaches and Recommendations

  Next-Generation Sequencing (NGS) has transformed cancer research and clinical practice, with Whole Exome Sequencing (WES) driving advances in mutational profiling and personalized oncology. Yet, transcriptomic signatures remain essential for understanding disease mechanisms, including therapy resistance pathways. RNA sequencing (RNA-seq), however, faces unique challenges when dealing with low-input or degraded RNA, as often found in archival formalin-fixed paraffin-embedded (FFPE) tissues. Although previous studies have compared library preparation protocols, rapidly evolving technologies call for updated evaluations. Here, we present a direct comparison of two FFPE-compatible stranded RNA-seq library preparation kits: TaKaRa™ SMARTer® Stranded Total RNA-Seq Kit v2 (Kit A) and Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Kit B). Both kits generated high-quality RNA-seq data, yet important differences emerged. Notably, Kit A achieved comparable gene expression quantification to Kit B while requiring 20-fold less RNA input, a crucial advantage for limited samples, albeit with increased sequencing depth. We critically discuss these results in relation to RNA availability, technical performance, cost-effectiveness, processing time, and automation potential, offering practical guidance for selecting optimal RNA-seq strategies in clinical and translational research settings

  Study EGAS50000001066

• Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Sequence reads for pediatric GBM samples for manuscript: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Dataset EGAD00001000134

• WES files for Newman MAP3K8 melanoma

  WES files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004566

• WGS files for Newman MAP3K8 melanoma

  WGS files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004579

• Exome and RNA seq data for female patient

  Exome and RNA sequencing data for EGAS00001003776 - one female patient with neurofibroma/schwannoma hybrid nerve sheath tumor (N/S HNST)

  Dataset EGAD00001005249

• RNA sequencing study for 8 pairs of primary NSCLCs and distant metastases

  RNA sequencing study for 8 pairs of primary NSCLCs and distant metastases. This dataset includes a total of 29 samples.

  Dataset EGAD00001005765

• MissionBio files for paper titled "Genomic Landscape and Clonal Architecture in Pediatric Myeloid Neoplasms with Chromosome 7 Deletions"

  MissionBio files for Klco paper titled "Genomic Landscape and Clonal Architecture in Pediatric Myeloid Neoplasms with Chromosome 7 Deletions"

  Dataset EGAD00001015493

• ESGI - Whole Genome Sequencing of samples from the Cilentogen isolates (2019-08-19)

  Deep whole genome sequencing of sampels from the Cilento isolates. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005266

• Transcriptomic profiling of the Enteric Nervous System in Hirschsprung Disease (2025-07-31)

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease. . This dataset contains all the data available for this study on 2025-07-31.

  Dataset EGAD00001015667

• Single nucleus and spatial transcriptomic characterization of prostate cancer versus normal controls

  10x Genomics Visium and Chromium platforms were used for spatial and single-nuclei RNA-sequencing, respectively. Cohort consisted of 8 prostate cancer patients (8 prostate cancer + 8 paired non-malignant control samples, fresh-frozen)

  Study EGAS50000001143

• March 2018 cumulative data release for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2018 cumulative data release (bams,fastqs) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium

  Dataset EGAD00001003963

• Exome and RNA sequencing data for Diffuse Large B Cell Lymphomas

  Exome sequencing data for 1001 DLBCL patients and RNA sequencing data for 775 DLBCL patients

  Dataset EGAD00001003600

• Inserm U1231 GAD TEAM

  This Data Access Committee reviews requests for access to the data submitted by the Inserm U1231 – Team GAD research team.

  Dac EGAC50000000707

• Mater Research Translational Bioinformatics DAC

  Data Access Committee for controlled-access sequence data published by the Translational Bioinformatics Group at the Mater Research Institute (Brisbane, Australia).

  Dac EGAC50000000755