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• sWGS on cfDNA and matching tumor DNA in pediatric cancer

  This dataset contains shallow whole genome sequencing data from paired cfDNA - tumor DNA samples of various pediatric cancer entities (total 215 samples). Files are provided in fastq format. Samples were sequenced on an Ion Proton sequencer (Thermo Fisher Scientific) or a Hiseq3000 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Dataset EGAD00001007508

• The genomic echoes of the last Green Sahara on the Fulani and Sahelian people

  Study EGAS00001007499

• Dataset for Fragle Software Development and Evaluation

  Fragle is a deep learning based two stage model that quantifies ctDNA from blood plasma derived cfDNA bam files. Fragle was developed using some previously published datasets and some newly generated data. Fragle was evaluated using some validation cohorts and some unseen cohorts. Some of these cohorts are newly created consisting of total 365 low pass (2-3X) whole genome sequencing bam files mapped to hg19/GRCh37. This dataset contains these newly generated bam files.

  Dataset EGAD50000000167

• INTEGRATIVE MOLECULAR ANALYSIS OF SKIN TUMORS FROM CYLD CUTANEOUS SYNDROME PATIENTS

  CYLD cutaneous syndrome (CCS) is a rare autosomal dominant disorder characterized by germline CYLD mutations and by multiple benign skin tumors dependent on NF-kB pathway. We assembled a large cohort of CCS rare skin tumors that was profiled with whole exome or genome sequencing, RNA sequencing and methylation arrays to better understand genetic mechanisms of CCS tumorogenesis.

  Dataset EGAD50000000362

• IgM VDJ repertoire sequencing of 3 healthy donors using 8 different PCR conditions

  Peripheral blood mononuclear cells (PBMCs) were sampled from 3 healthy donors to sequence IgM heavy chain V(D)J repertoire libraries. Libraries were generated by targeting IgM heavy chain V(D)Js with a 5’MTPX primerset and sequenced on an Illumina MiSeq machine. Each donor was sequenced 8 times, varying only PCR amplification conditions, for a total of 24 sequencing libraries and therefore 48 paired-end fastq files.

  Dataset EGAD50000001510

• B cells (CD19) RNAseq dataset of JIA patients with known uveitis status.

  CLUSTER consortium RNA sequencing dataset from UK JIA patient cohort with documented uveitis status. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples and cryopreserved. Samples were subsequently thawed and flow-sorted for CD19+ B cells prior to RNA sequencing. Clinical metadata includes patient demographics and uveitis status at time of sampling.

  Dataset EGAD50000001616

• RNASeq of OvCa

  RNAseq data relative to 56 primary and treatment-naive ovarian carcinomas, from independent donors.

  Dataset EGAD00001008547

• iPSC and iNeuron RNAseq, chip-seq and single cell CRISPR activation

  Dataset includes 1) RNAseq for Bob_Ngn2 cell differentiation from iPSC to iNeuron stage (time point 0, 24, 48 and 96 hours). 2) Bob_Ngn2 cell line chip-seq (H3K4me3, H3K4me1, H3K27me3, H3K9me3, H3K27ac, H3K36me3) for both iPSC and iNeuron stage with 3 replicates at each time point. 3) Single cell CRISPR activation experiment with 96 endogenous genes.

  Dataset EGAD00001010050

• TRACERx pilot study.

  Multi-region Illumina whole-exome and/or whole-genome sequencing on tumor regions collected from early-stage NSCLC patients who underwent definitive surgical resection prior to receiving adjuvant therapy.Detected variants were validated on Ion AmpliSeq™ Custom Panel and/or Comprehensive Cancer Gene Panels.Patients covered by this dataset: L001, L002, L003, L004, L008 and L011.

  Dataset EGAD00001000900

• Pancreatic Cancer Sequencing Initiative

  Pancreatic Cancer Sequencing Initiative for the International Cancer Genome Consortium at the Ontario Institute for Cancer Research.

  Study EGAS00001000343

• methylation_mifepristone_set

  Raw methylation from breast biopsies in BRCA mutation carriers or controls before and after 3 months of preventive mifepristone treatment.

  Dataset EGAD00010002073

• scRNAseq: Human periportal liver assembloids recapitulate periportal liver tissue in vitro

  Sample number: 8 Sample details: Total 8 samples, including Homeostatic-like assembloids (4 samples), Fibrotic-like assembloids (4 samples).

  Dataset EGAD50000001453

• Primary Neuroblastoma Circle-seq Data

  Circle-seq data for 21 primary neuroblastoma samples supporting Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020).

  Dataset EGAD00001006580

• NiCOL Study Target-seq dataset

  10 samples sequenced in Target-sequencing of a panel of 571 genes (Illumina NovaSeq 6000) - Raw FASTQ data - Annotated VCF

  Dataset EGAD00001010911

• DNMT3A MOPD patient ChIP-seq data

  ChIP-seq data from controls and patients with de novo DNMT3A mutations resulting in microcephalic primordial dwarfism.

  Dataset EGAD00001004473

• Germline whole exome sequencing in testicular cancer

  This dataset contains variant call format files generated from whole exome sequencing of germline DNA from indiviudals with diagnosed with testicualr germ cell cancer.

  Dataset EGAD00001004345

• Whole exome sequencing dataset in follicular lymphoma without evidence of transformation

  Whole exome sequencing data of 5 patients diagnosed with FL that had undergone several relapse episodes without evidence of transformation

  Dataset EGAD00001001301

• 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

• Rio Dataset

  Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer. RNA-Seq data for paired baseline and end of treatment samples

  Dataset EGAD00001006120

• RNA-Seq data from tumor samples collected from 12 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates differentially expressed genes associated with the progression of translocation renal cell carcinoma (tRCC) by analyzing RNA-Seq data from 23 tumor samples obtained from 12 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. RNA isolated from tumor samples was sequenced using the Illumina platform.

  Study EGAS50000000127

• MicroRNA Biomarkers for Prediction of Preeclampsia

  Maternal serum was collected between 17-28 weeks gestation. Samples were obtained from the high-risk Placental Study at the University of California, San Diego (n=48) and from the average-risk Proteomic Assessment of Preterm Risk (PAPR) Study at Sera Prognostics (n=164). RNA was extracted from 500 microliter of maternal serum using the miRNeasy Micro kit (Qiagen). NEBNext Small RNAseq Library Preparation Kit was used for library construction.

  Study phs002016

• IBD_Whole_Genome_Sequencing

  We will sequence at 15X coverage the genomes of 1536 IBD patients. These samples are currently onsite at Sanger and made available for sequencing via our collaboration with the UK IBD Genetics consortium. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002238

• Reconstructed VDJ sequences from Smart-seq2 data

  The dataset contains reconstructed VDJ sequences (fasta files) and accompanying metadata for each cell (csv file) from scRNA-seq data generated with the Smart-seq2 protocol. The VDJ sequences were reconstructed with the computational tool BraCeR using raw fastq files as input. The dataset contains sequences from 355 IgA+ peripheral blood B-lineage cells of two untreated celiac disease patients. The sequences comprise both IgA+ transglutaminase 2-specific and other IgA+ B cells.

  Dataset EGAD50000000341

• Cardiometabolic effects of Anaerobutyricum soehngenii

  This study investigated the effects of the probiotic strain Anaerobutyricum soehngenii on plasma metabolites and cardiometabolic parameters. Strain engraftment was determined through strain tracking of fecal metagenomics. Plasma metabolites levels were determined using untargeted metabolomics. Additionally the interaction with metformin dose was studied.

  Study EGAS50000000415

• single cell RNA-seq of small cell lung cancer tumors

  This study investigated the transcriptomic profile of small cell lung cancer from 10 patients. Tumors were rapidly dissociated after the surgical procedure. Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit. Samples were sequenced on a NextSeq 550 sequencer (Illumina).

  Study EGAS50000001400

• HaJo Cell Line WES Data

  This study includes whole-exome sequencing data of the HaJo cell line and the corresponding patient and PDX samples.

  Study EGAS50000001432

• HaJo Cell Line WTS Data

  This study includes Whole-Transcriptome Sequencing Data of the HaJo cell line including the corresponding patient and PDX data.

  Study EGAS50000001433

• HaJo Cell Line BCRseq Data

  This study includes BCRseq data from the HaJo cell line as well from the corresponding patient and PDX samples.

  Study EGAS50000001434

• ESGI___Whole_Genome_Sequencing_of_samples_from_the_Croatian_isolated_populations_

  Whole genome sequencing of sampels from isolated populations from Croatia. The samples are sequenced using the Illumina HiSeq X Ten system.

  Study EGAS00001001119

• Epigenomic profile of diverse cancer

  The samples are from patients of multiple cancer types. The library preparation protocol was developed by the laboratory. The DNA libraries were then sequenced with 150bp paired-end reads.

  Dataset EGAD00001006124

• The genomic VCF data of the comprehensive proteogenomic characterization of early-stage DC project

  The genomic VCF data of the Integrative proteogenomic characterization of early-stage DC project ,this dataset contains 76 VCF files.

  Dataset EGAD00001008987

• Project MinE Illumina Infinium HumanMethylation450 (450k) BeadChip data on 2,790 Dutch whole blood samples, including 1,761 ALS patients of which 119 are known carriers of the C9orf72 repeat expansion.

  This dataset includes IDAT files from 2,790 blood samples. The samples were profiled using the Illumina Infinium HumanMethylation450 (450k) BeadChip.

  Study EGAS00001004587

• Precision Interception of Gastric Cancer Precursors Through Molecular and Cellular Risk Stratification

  The GAstric Precancerous conditions Study (GAPS, NCT04191551) is a cross-sectional study of patients undergoing endoscopy who are at increased risk of gastric cancer. Enrolled patients are administered a standardized questionnaire, undergo clinical biopsy collection using the Sydney system, and consent for the collection of saliva, blood, and additional gastric tissue. All patients are scored for intestinal metaplasia using the operative link on gastric intestinal metaplasia (OLGIM) scoring system.

  Study phs003648

• Whole Genome Sequencing from patients with multiple myeloma treated with BCL2 inhibitor based treatment

  Samples was collected at the Mayo Clinic. MM tumor samples were enriched using the StemCell EasySep Human CD138 positive selection kit II (StemCell, Cambridge, MA). DNA from CD138+ MM cell (tumor) or peripheral blood samples (germline control) at Mayo Clinic (Rochester or Arizona) underwent WGS. For samples collected at Mayo Clinic Rochester, library preparation was completed using the NEB Ultra II (New England Biolabs, Ipswich, MA) and the Nextera Flex systems (Illumina, San Diego, CA) and sequenced at the Mayo Clinic Genome Analysis Core with an approximate depth of 30X for tumor samples and 60X for the germline control. For samples collected at Mayo Clinic Arizona, Novogene was used for WGS following random shearing of the DNA, end-repairs, A-tailed and ligated with Illumina adapters. Sequencing was performed on the Illumina Novaseq 6000 sequencer Reference Genome: GRCh38.

  Dataset EGAD50000002132

• Cell-free DNA sequencing data of healthy control, atrophic gastritis, and gastric cancer patients’ blood

  Sample cohort (n=48) is consisted of healthy, atrophic gastritis and gastric cancer patients. Some of the gastric cancer patients samples are collected at the separate time points: -1 before the operation; -2 after the operation; -3 during the control visit. For the hybridisation capture of the genes unique 15 gastric cancer-related gene panel was developed and very deep sequencing using TruSight Oncology Unique Molecular Identifier (UMI) Reagents (Illumina) was used.

  Dataset EGAD00001011153

• ESGI - Whole Genome Sequencing of NSPHS samples (2019-08-19)

  Whole genome sequencing of sampels from the NSPHS cohort. 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 EGAD00001005267

• The genomic VCF data of the Integrative proteogenomic characterization of early esophageal cancer project

  The genomic VCF data of the Integrative proteogenomic characterization of early esophageal cancer project ,this dataset contains 90 VCF files.

  Dataset EGAD00001008672

• NHLBI TOPMed: Genetic Causes of Complex Pediatric Disorders - Asthma (GCPD-A)

  The Center for Applied Genomics (CAG) at the Children's Hospital of Philadelphia (CHOP) is focused on addressing the roles of both single nucleotide variants and structural copy number variants, and their functional impact, together with gene-environment interactions and their influence on asthma drug response.

  Study phs001661

• BCC HHI-ICI combination therapy

  Data of advanced basal cell carcinoma patients receiving hedgehog-inhibitor and immune checkpoint-inhibitor combination treatment. The single-cell RNA-sequencing data was generated via the Parse Biosciences platform from PBMC samples of 10 patients at 4 four timepoints each. The spatial transcriptomics dataset was generated using the 10x Visium platform (+CITE-seq) and contains altogether 10 biopsies at different timepoints during treatment from 3 patients. The processed matrices with the spatial images can be downloaded from: https://zenodo.org/records/17814765

  Dataset EGAD50000002134

• Whole_Genome_Sequencing_of_INTERVAL

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase II. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002461

• Whole_Genome_Sequencing_of_INTERVAL

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase III. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002787

• Bulk RNA sequencing of Singapore colorectal cancer patients (SG-BULK)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001005978

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-3)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006056

• Whole genome sequencing of colorectal cancer patients (SG-BULK-1)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006030

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-5)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006114

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-2)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006039

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-4)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006101