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• Paired-end Hi-C analysis of the 3D spatially mapped GBM samples.

  Dataset contains 21 paired-end Hi-C samples from 9 patients.

  Dataset EGAD00001010312

• RCRF release 1

  Transcriptome sequencing from the Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendocrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010198

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  Dataset EGAD00001010049

• mRNA-Seq dataset

  mRNA-Seq, HiSeq 2000 dataset of the Cell-line use case

  Dataset EGAD00001002250

• The UCSF Low Grade Glioma Genome Project #2"

  Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor

  Dataset EGAD00001001305

• EGYPT_HIGH_COVERAGE_vcf

  Integrated callset of high coverage Egyptian genomes from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j.ajhg.2015.04.019)

  Dataset EGAD00001003295

• Enhancing OSCC Prediction: The Prognostic Power of WPOI and Tumor Budding, and the Limited Impact of Molecular Resection Margins

  This dataset contains sequences with results of mutations observed in patients with oral squamous cell carcinoma. Mutations were detected by NGS in tumor tissue, tumor margins, and peripheral blood as a healthy control. Study was using a panel of 88 cancer-related genes, which were selected based on a literature search.

  Study EGAS50000000074

• TREM2+ Cells in Human Basal Cell Carcinomas

  To explore the tumor immune microenvironment heterogeneity in sporadic human basal cell carcinoma tumors, we profiled two individual patient tumors by scRNA-Seq. We identified a population of TREM2+ macrophages, which have been implicated in promoting an immunosuppressive tumor microenvironment. We identify that TREM2+ can promote tumor epithelial proliferation in an immunosuppressive independent manner.

  Study phs003242

• CALGB 80303:Genome-Wide Association Study of Advanced Pancreatic Cancer Patients - A Randomized Phase III trial of Gemcitabine Plus Bevacizumab versus Gemcitabine Plus Placebo in Patients with Advanced Pancreatic Cancer

  CALGB 80303 was a randomized, phase III study in advanced pancreatic cancer patients treated with Gemcitabine plus either Bevacizumab or placebo. No difference in overall survival (OS) was observed between the two arms. We prospectively collected germline DNA and conducted a genome-wide association study (GWAS).

  Study phs000250

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778

• Genomic characterization of a patient with AGS and CdLS transcriptomic comparison of his monocytes against healthy and disease control samples

  In this study, we describe an extreme genetic phenotype of two simultaneous genetic lesions, leading to broad alterations in immunophenotype and transcriptome. Whole Exome Sequencing and RNA-Sequencing of CD14+ monocytes was performed on the case patient, and RNA-sequencing was also performed on disease (Systemic Lupus Erythematosus) and healthy controls.

  Study EGAS00001007829

• Identifying and Reducing Disparities in Patient-Reported Outcomes Among African American Prostate Cancer Survivors

  This research study aimed to identify disparities in prostate cancer symptom burden and their contributors among African American, Hispanic, and non-Hispanic White prostate cancer survivors. We collected patient-reported outcomes data, focusing on various aspects of the survivors' health and well-being, clinical data, demographics data, and germline genomic data.

  Study phs003745

• Single-cell genotype-to-phenotype (scG2P) data of single nuclei from cell line mixing experiment and six donors

  We developed Single-cell genotype-to-phenotype (scG2P) to profile mutations in driver gene hotspots and capture mRNA targets of interest, validating this assay in a cell line mixing experiment of KYSE-270, KYSE-410, and HCT-116, and applied the assay to esophageal biopsy samples from six donors.

  Study EGAS50000001429

• Immunoreactive_p53_areas_in_human_skin_2

  Previous work has suggested that in mice there may be a difference in mutational burden between areas expressing stabilised p53 protein and others. We wish to see if this observation holds true in human sun-exposed epidermis. We will take 0.25mm punch biopsies from peeled human skin epidermis which will be submitted to the low input pipeline prior to sequencing.

  Study EGAS00001004463

• RNAseq_Pulldown_

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. In this experiment cDNA derived form Breast Cancer Cell lines was used in an Agilent whole exome pulldown experiment.

  Study EGAS00001000230

• ChIP-seq analysis of clear cell renal cell carcinoma

  In order to understand the epigenetic basis on ccRCC, we performed ChIP-seq on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. This study analysed data from H3k4me1, H3K4me3, H3K27ac, H3k27me3, H3k36me3, CTCF, and HIF1A

  Study EGAS50000001322

• Triple_Negative_Breast_Cancer_Whole_Genome_Validations

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found.

  Study EGAS00001000426

• Gene expression in brain (Schizophrenia) study

  The study included post-mortem brain tissue samples from 68 schizophrenia patients and 44 age and sex matched control subjects. Whole transcriptome poly-A selected paired-end RNA sequencing was performed on tissue from prefrontal cortex and orbitofrontal cortex. RNA expression differences were detected between case and control individuals, focusing both on single genes and pathways.

  Study EGAS00001004199

• Profiling of H3K27ac landscape in immune cells from rheumatoid arthritis patients and healthy controls

  We collected peripheral blood mononuclear cells (PBMC) from 6 RA patients and 4 healthy controls, as well as synovial fluid from the same RA patients. We then sorted B cells, CD4+ and CD8+ T cells, regulatory T cells and monocytes using flow cytometry and profiled regions marked with H3K27ac using CUT&Tag.

  Study EGAS00001005085

• scRNA-seq to study interactions between HSPCs, BMSCs and immune microenvironment

  Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

  Study EGAS00001008181

• Single nucleus and bulk transcriptomics in prefrontal cortex of individuals with alpha synucleinopathies

  We explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single nucleus RNA sequencing using 10X Genomics, and bulk RNA sequencing from the prefrontal cortex of individuals with alpha synucleinopathies - Parkinson's Disese (PD), monogenic LRRK2 PD, and multiple system atrophy (MSA), together with neurologically healthy controls.

  Study EGAS50000000301

• WGS data of paediatric T-ALL acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one T-ALL patient (ALLK-118), and relapse (from BM and tonsil) and matched remission (control) samples of another T-ALL sample (ALLT-317, tonsil relapse ALLT-3107L). Diagnostic sample of ALLT-317 in the first dataset in this submission. Sequencing library was made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic/relapse (90x) and remission (30x) samples were sequenced using Illumina Novaseq 6000.

  Dataset EGAD50000002014

• PRO-SPeCT: PROstate cancer heterogeneity deconvolution through Single cell Profiling of Chromatin accessibility and Transcriptomic output

  38 prostate cancer specimens derived from five human patients with ISUP ≥ 3 pathology who underwent radical prostatectomy and pelvic lymph node dissection at surgery as part of the International Cancer Genome Consortium (ICGC) late-onset cohort. Using single-cell multiome (expression and chromatin accessibility from RNA and ATAC, respectively) sequencing assay, we characterized 282,956 nuclei/cells, with a median of 6 primary tumor foci from the prostate gland and 3 locoregional lymph node metastases across all patients.

  Dataset EGAD50000000745

• Poland WES - The Genomic Map of Poland in Open Access

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Exome Sequencing of 450 samples (227 female, 223 male, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA Prep with Enrichment. Reference Genome: GRCh37.

  Dataset EGAD50000000130

• Paired RNA-Seq was performed on 125 samples of low grade pediatric glioma

  Paired RNA-Seq was performed on 125 samples of low grade pediatric glioma. The sequencing was done with Illumina Novaseq 6000 and the Illumina TruSeq stranded mRNA kit.

  Dataset EGAD00001010171

• Cell-free DNA and bone marrow samples from myelodysplastic syndromes

  We have assessed the molecular profile of a cohort of 70 patients with MDS by next-generation sequencing (NGS) using cfDNA and compared the results to paired bone marrow (BM) DNA.

  Dataset EGAD00001008567

• Exome sequencing samples from the Acute Care Flagship.

  Exome sequencing samples from the Acute Care Flagship, Illumina sequencing.

  Dataset EGAD00001008105

• Targeted Germline Sequencing of the Leeds Melanoma Cohort

  In this project we performed targeted sequencing of known and suspected melanoma susceptibility genes in a cohort of melanoma patients and matched controls. Our aim was to identify variants that predispose to melanoma development. The melanoma cases used in this study were population ascertained.

  Dataset EGAD00001007520

• Exome sequencing of matching primary tumor and venous tumor thrombus (VTT) renal cell carcinoma (RCC) samples

  We performed multiregion whole exome sequencing of a total of 37 samples from five consecutive patients (normal tissue, n=5; primary tumors, n=16; tumor thrombi, n=16) to >35-fold target coverage. Matching primary tumor and venous tumor thrombus samples were analyzed. Four patients had a clear cell RCC, one patient had a poorly differentiated type II papillary RCC (RCC-VTT-04). The latter patient had a friable thrombus, the others were of solid consistency.

  Dataset EGAD00001004887

• VCF dataset of Colorectal Cancer Synthetic genomes

  This dataset contains genomic variants data from VCF files of four patients synthetically generated in the EOSC4Cancer project

  Dataset EGAD50000000314

• Papua New Guinea Pangenome Project Data Access Policy

  This data policy applies to data access to the PNG15 and PNG16 sequencing data as well as derived genomic variant calls.

  Dac EGAC50000000674

• CD4 auto-antigens

  The CD4 auto-antigen Access Committee (DAC) manages and oversees data access, ensuring compliance with ethical and regulatory guidelines while facilitating secure sharing with authorized researchers.

  Dac EGAC50000000864

• cfRRBS data plasma healthy donor

  cfRRBS data produced from the cfDNA in plasma isolated from healthy, adult donors.

  Dataset EGAD50000000553

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  spatial transcriptomics

  Dataset EGAD00001015262

• 46 VCF files of glioma patient 2021

  the source data in VCF format of 46 patients primary malignant glioma cohort in Chinese population

  Dataset EGAD00001008115

• Mapping the breast cancer metastatic cascade onto circulating tumour DNA using genetic and epigenetic clonal tracking

  Dataset EGAD00001005507

• Cloning of the breakpoint of a novel translocation associated with T-acute lymphoblastic leukaemia

  Single case of T-ALL carrying t(4;6), a novel translocation.

  Dataset EGAD00001002193

• The Ashkenazi Genome Consortium: Phase I

  Whole genome, high coverage, sequencing of 128 Ashkenazi Jewish controls

  Dataset EGAD00001000781

• PBAT sequencing of human embryonic stem cells

  To assess the DNA methylation landscape of naïve human embryonic stem cells derived from ERKi or control blastocysts using PXGL or UXGL media.

  Dac EGAC50000000606

• Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin

  Study EGAS00001004660

• LEMA WES files

  This dataset contains WES bam/bai files associated with 133 patients as part of the LEMA Study

  Dataset EGAD50000001311

• ACUITI BAM files

  This dataset contains WES bam/bai files associated with 51 patients as part of the ACUITI Study

  Dataset EGAD50000001401

• Data used in "BaTwa" populations from Zambia retain ancestry of past hunter-gatherer groups

  BaTwa genotype data using the H3Africa array.

  Dataset EGAD50000000555

• STAG1-ChIP-Seq of STAG2-mutated and cohesin wildtype adult AMLs

  ChIPseq targeting the cohesin subunit STAG1 in STAG2-mutated AMLs or cohesin wildtype AMLs

  Dataset EGAD00001011206

• Covacta OLINK LOD

  Explore 1536 dataset from serum of patients enrolled in the COVACTA trial. This dataset includes limit of detection values provided by Olink.

  Dataset EGAD00001011161

• Plasma methylome of metastatic prostate cancer

  The dataset contains plasma DNA methylation data derived from metastatic prostate cancer patients.

  Dataset EGAD00001005433

• GWAS_HPI_Lund

  Genotyping data (Imputed) from human pancreatic islets from 191 donors from Lund that were analysed as part of the Inspire consortium.

  Dataset EGAD00001005521

• 300-Obese cohort gut microbiome data

  300-Obese cohort, Nijmegen, the Netherlands. Dataset contains gut microbiome data generated by metagenomic sequencing.

  Dataset EGAD00001005083

• GCLJ RNA-Seq data

  RNA-Seq data from 6 Giant Cell Lesions of the Jaw (GCLJ) samples.

  Dataset EGAD00001004320

• Myeloproliferative Neoplasms (MPN) Exome Validation Study

  Experiments using targeted pulldown methods will be sequenced to validate findings in the exomes of patients with Myeloproliferative Neoplasms (MPN).

  Dataset EGAD00001000619