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• CCA Visium spatial transcriptomics data (4 CCA)

  Visium spatial transcriptomics (10X Genomics) performed on 4 CCA samples. Each sample has two paired-end sequencing runs: the first (I1 & I2) are a pair reading indexes; the second (R1 & R2) are a pair reading inserts, with R1 additionally reading 10X barcodes. For histology images, please contact authors.

  Dataset EGAD00001011997

• Neoantigen responses to Immunotherapy in Prostate Cancer

  To determine whether antigen-specific T cell responses can be elicited following treatment with ICT in cancers that have a low TMB, a clinical trial with ipilimumab (anti-CTLA-4) was conducted in 30 patients with metastatic castration-resistant prostate cancer (CRPC). We identified 2 distinct groups of patients divided by clinical outcomes, which consisted of a cohort with Favorable and Unfavorable outcomes. Compared to the Unfavorable cohort, the patients in the Favorable cohort were more likely to have higher intratumoral CD8 T cell density and/or IFN-γ response gene signature, including five patients who had antigen-specific T cell responses that were only detectable after ipilimumab therapy. Three patients had T cell responses against tumor-associated antigens (PSMA and PAP). Importantly, two patients with a relatively low TMB had T cell responses against unique neoantigens. Collectively, our data indicate that a subset of patients with metastatic prostate cancer benefit from ICTs, particularly those who have immunological biomarkers associated with effector T cell responses. Publication: Sumit K. Subudhi, Luis Vence, Hao Zhao, Jorge Blando, Shalini S. Yadav, Qing Xiong, Alexandre Reuben, Ana Aparicio, Paul G. Corn, Brian F. Chapin, Louis L. Pisters, Patricia Troncoso, Rebecca Slack Tidwell, Peter Thall, Chang-Jiun Wu, Jianhua Zhang, Christopher L. Logothetis, Andrew Futreal, James P. Allison and Padmanee Sharma, 2020, Neoantigen responses, immune correlates, and favorable outcomes after ipilimumab treatment of patients with prostate cancer. Science Translational Medicine, 01 Apr 2020:Vol. 12, Issue 537, eaaz3577DOI: 10.1126/scitranslmed.aaz3577. https://pubmed.ncbi.nlm.nih.gov/32238575/

  Study EGAS00001004050

• GnRH Agonist-Induced Ovarian Suppression and Ovarian Steroids in PMDD and Controls

  In this study, lymphoblastoid cell line cultures (LCLs) from women with premenstrual dysphoric disorder (PMDD) and asymptomatic controls were compared via whole-transcriptome sequencing (RNA-seq) during untreated (ovarian steroid-free) conditions and after estradiol and progesterone treatment. In untreated LCLs, pathway analysis of the LCL transcriptome revealed, among others, over-expression of ESC/E(Z) complex genes (an ovarian steroid-regulated gene silencing complex) with significant overexpression of MTF2, PHF19, and SIRT1 (P<0.05) in cells from women with PMDD compared with controls. Finally, mRNA expression of several ESC/E(Z) complex genes were increased by progesterone in controls only, and decreased by estradiol in PMDD LCLs.

  Study phs001344

• National Heart, Lung, and Blood Institute (NHLBI) Bench to Bassinet Program: The Pediatric Cardiac Genetics Consortium (PCGC)

  Multi-center, prospective observational cohort study of individuals with congenital heart defects (CHD). Phenotypic data and source DNA derived from 10,000 probands, parents, and families of interest are being collected to investigate relationships between genetic factors and phenotypic and clinical outcomes in patients with CHD.

  Study phs000571

• Nurminen et al ("GP2Men") Study Primary and Metastatic Prostate Cancer Whole Genome Sequence Data

  We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones.

  Dataset EGAD50000000005

• Exome data from 154 patients with childhood or adolescent cutaneous melanoma

  This dataset contains sequence data from 154 patients in Australia diagnosed with cutaneous melanoma before the age of 20. Each patient was exome sequenced on the illumina platform. Generated sequence reads were aligned against version 19 of the human genome assembly and stored in bam files made available here.

  Dataset EGAD50000001868

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10345i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003107

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003108

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10592i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003109

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10679iA

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003110

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003111

• Chromosomally integrated HHV6 data of parent-infant pairs

  Raw data used in the analysis of chromosomally integrated HHV6 genomes in parent-infant pairs, generated by means of full viral genome sequencing by SureSelect target enrichment, in the context of a larger study investigating the relationship between HHV6 and adverse pregnancy outcome.

  Dataset EGAD00001004592

• Single cell mRNA sequencing of primary GBM - SF 10282

  We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002270

• Single cell mRNA sequencing of primary GBM - SF 10360

  We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002272

• Single cell mRNA sequencing of primary GBM - SF 10345

  We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002271

• Tumor evolutionary trajectories during the acquisition of invasiveness in early stage lung adenocarcinoma

  Genomic analysis between pre-invasive and invasive components of malignant pulmonary nodule (MPN) facilitates the description of lung adenocarcinoma (LUAD) evolutionary patterns. We conduct an analysis of gene-panel sequencing on 53 T1 stage LUAD cases, which extend the understanding of evolutionary trajectories during invasiveness acquisition in early LUAD.

  Dataset EGAD00001006457

• Whole exome sequencing in patients with ALS and concomitant FTD lacking the C9orf72 repeat expansion

  Dac EGAC00001000656

• Effect of aging on chromatin accessibility and gene expression in immune cells, The Jackson Laboratory

  Dac EGAC00001000721

• The European MAPPYACTS trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

  Dac EGAC00001003276

• Genomic validation of the revised Bethesda criteria in terms of pathogenesis and oncologic significance

  Study EGAS00001003959

• Genotype data from 'Evidence of the interplay of genetics and culture in Ethiopia'

  Study EGAS00001005171

• Batch-corrected read-count matrix of the RNAseq Datasets of CLUSTER JIA pre-MTX cohort

  Samples were sequenced with NovaSeq6000 and the sequencing files were processed using the RSSnextflow workflow (https://gitlab.com/b8307038/rssnextflow). The raw read counts from all batches were combined. Analysis-ready batch-corrected read counts were generated using ComBat-seq.

  Dataset EGAD50000002169

• Single-cell transcriptomic analyses of peripheral blood mononuclear cells from patients with colorectal cancer metastasized to the peritoneum

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peripheral blood mononuclear cells (PBMC) from patients with colorectal cancer (CRC) and peritoneal metastases (PM). Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000247

• H3Africa AWI-Gen Phase 1 WGS data from 100 South Africans

  These samples were sequenced at the Broad Institute on an Illumina HiSeqX at 30x -- PCR Free. The CRAMS and VCF are as produced by Broad. The VCFs produced were generated by the Broad using GATK.

  Dataset EGAD00001006418

• RNAseq_pituitary_adenoma

  Total RNA was extracted using RNAble (Eurobio), cleaned-up with RNeasy columns (Qiagen) and sequenced. The libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq Stranded mRNA protocol (Illumina), starting from 1 µg of high quality total RNA. Paired end (2 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on hg19 (GRCh37) human reference genome with STAR (v.2.5.2a)

  Dataset EGAD00001004996

• GNAI1 CGH Array

  The cytogenetic analysis of probands was performed with a result of normal male karyotypes (46,XY). The microarray analysis on oligonucleotide 180K CGH+SNP microarray platform was then indicated resulting in a detection of a 8q24.23q24.3 duplication (694 kb) in both probands. The family-based real-time PCR confirmed this CNV in both probands and their unaffected mother. Based on the information obtained from databases mentioned above it was classified as likely benign.

  Dataset EGAD00001007742

• RNASeq of Calcoco2 in beta and fat cell lines

  Investigation of the function of Calcoco2 by knocking it down in beta and fat cell lines.

  Dataset EGAD00001008654

• Observational study on the immune responses acquired by COVID-19 convalescent individuals

  We performed whole exome sequencing and microarray genotyping analysis of rare disease A two patients. .....

  Study JGAS000563

• WES in Angolan and Cape Verdean triple-negative breast cancer samples

  WES (using the SureSelect Human All Exon V5 + UTRs target enrichment kit) in 23 Angolan and 7 Cape Verdean triple-negative breast cancer samples

  Dataset EGAD50000001482

• Whole Genome Sequencing of tumor and blood from 4 pediatric cases with second malignancies.

  Whole Genome Sequencing (120X) of the two tumors and blood from 4 pediatric cases with second malignancies (12 WGS)

  Dataset EGAD50000000237

• Methylation profiling of CDS and ES tumor samples

  Methylation profiling of 9 CDS and ES tumor samples, using the approach described in "Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target

  Dataset EGAD00010002760

• Microbial infections in Alzheimer’s patients

  In the present study, we have examined fungal and bacterial infection in brain tissue from 10 AD patients and 16 control subjects by next-generation sequencing NGS using MiSeq sequencing platform (Illumina).

  Dataset EGAD00001003886

• Case Report of a Leukemic Patient with Invasive Mucormycosis

  Whole exome sequencing of germline DNA was performed and subsequent polymorphisms in genes known and putatively involved in the innate immune response to fungi were identified

  Dataset EGAD00001001692

• Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing

  The dataset comprises of muscle samples from three patients with mitochondrial disease: Patient 1, age9; Patient 2, age16; and Patient 3, age 58.

  Dataset EGAD00001006079

• Macrophage response in term and preterm infants

  The data set comprises 48 samples from term and preterm infants. Expression profiles were generated using different stimuli (O2 3%, 21%, 65%; LPS stimulation).

  Dataset EGAD00001006885

• Canadian Prostate Cancer Genome Network

  Over 5 years, CPC-GENE will sequence the genomes of 350 intermediate risk prostate cancers to identify genetic signatures that differ in cancers that responded well to treatment compared with those that did not. CPC-GENE will also sequence multiple regions of prostate cancer from the same gland to determine if and how the genetic make-up of prostate cancer varies within an individual man’s prostate

  Study EGAS00001000900

• RNAseq and ATACseq data, derived from HGSC cell lines pre- and post- treatment with an epigenetic compound

  These data consist of transcriptome and chromatin accessibility data (RNAseq and ATACseq respectively) derived from five High-Grade Serous Ovarian Carcinoma (HGSC) cell lines. HGSC lines included PEO1, PEO4, PEA2, OVCAR5 and OVCAR8. Samples were taken pre- and post-treatment with a novel epigenetic compound, HKMTi-1-005, which targets the activity of two histone methyltransferases, EZH2 and G9a.

  Dataset EGAD50000000064

• COVID-19 Outpatient Thrombosis Prevention Trial (ACTIV-4B)

  An adaptive randomized double-blind placebo-controlled platform trial to compare the effectiveness of anticoagulation with antiplatelet agents and with placebo to prevent thrombotic events in patients diagnosed with COVID-19 who are not admitted to hospital as COVID-19 related symptoms are currently stable.

  Study phs002710

• Treatment of CAR T cells with immunomodulatory metabolites

  Anti-Her2-CAR T cells produced from T cells derived from healthy human donors were treated with DMSO (control) or either of the immunomodulatory metabolites indole‐3‐carboxaldehyde (ICA), valeric acid (VA) and isovaleric acid (IVA) to assess effects on CAR T cell function.

  Study EGAS50000001386

• metastatic uveal melanoma tumour biopsies

  Tumour biopsies were obtained from uveal melanoma patients pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Study EGAS50000000864

• metastatic uveal melanoma tumour biopsies (n=35)

  Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Study EGAS50000000836

• A living biobank of patient-derived ductal carcinoma in situ Mouse-INtraDuctal xenografts identifies factors associated with risk of invasive progression

  Create a living biobank of patient-derived ductal carcinoma in situ (DCIS) Mouse-INtraDuctal (MIND) xenografts to find factors explaining invasive growth. Samples exist of both primary and pdx samples. Invasive growth was scored in the pdx.

  Study EGAS00001006554

• mRNA-seq of in vitro differentiation from induced pluripotent stem cells to hepatocyte-like cells

  Fastq files of mRNA-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE) and hepatocyte-like cells (HLC). The dataset comprises data from the in vitro differentiation protocol Cellartis (Takara Bio, "CEL", n = 4) and several interventions (11x3 replicates).

  Dataset EGAD00001005935

• Single circulating tumor cells in hepatocellular carcinoma

  We determined intra- and inter-vascular transcriptional heterogeneity within the circulatory system using single-cell RNA-sequencing of 113 CTCs isolated from four key vascular sites along their dissemination route in ten HCC patients. The dataset consists of 146 paired-end fastq files from 113 sigle CTCs, HuH-7 cell line, Hep3B cellline, white blood cell, tumor and normal bulk tissue.

  Dataset EGAD00001007642

• Single-cell RNA-seq data of bronchoalveolar lavage (BAL) fluid in severe COVID-19 and SARS-CoV-2 stimulated classical blood monocytes

  We performed single-cell RNA-sequencing of cells in the bronchoalveolar lavage (BAL) fluid of severe COVID-19. In addition, we performed single-cell RNA-sequencing of SARS-CoV-2 stimulated classical blood monocytes. This study provides detailed insights into the alveolar macrophage response to SARS-CoV-2 infection and reveals a profibrotic macrophage response in severe COVID-19 patients.

  Dataset EGAD00001006827

• Multiple myeloma follow-up Dataset

  77 samples collected from 35 multiple myeloma patients. Each patient provided one healthy sample and one primary tumor sample and, in some cases, also samples collected after the progression of the disease.

  Dataset EGAD00001010161

• RNA-Seq of GM adipose tissue samples

  This dataset contains 210 fastq files (RNA sequencing was performed in two centers) from 105 individuals (106 files in subcutaneous tissue and 104 files in visceral tissue). Of the 210 fastq files, 129 files are in PEx100 mode (appeared in a single fastq file) and 81 files are in PEx49bp mode (appeared in two separate fastq files). Sequencing was done on the Illumina HiSeq2000 platform.

  Dataset EGAD00001010253

• Immunogenomic analysis of tumor infiltrating B cells in gastric cancer

  Despite the accumulating evidences of the significance of humoral cancer immunity, its molecular mechanisms have largely remained elusive. This study aimed at profiling the global picture of the humoral cancer immunity in view of immune repertoire characteristics of tumor-infiltrating B cells. In this study, we investigated B-cell repertoire (BCR) / immunoglobulin (Ig) sequencing of tumor infiltrating B cells in 102 clinical gastric cancers. First, total RNAs were extracted from frozen gastric cancer tissues and corresponding normal gastric mucosa; then, BCR/Ig repertoires of tumor-infiltrating B cells were amplified by target PCR using multiplex primer sets available from iRepertoire(R), inc. Subsequent next-generation sequencing data obtained by the Illumina platform were aligned onto human BCR/Ig repertoire sequence. This dataset contains the repertoire sequencing data of 102 gastric cancer cases analyzed in this study.

  Study JGAS000242

• ChIP-seq peaks of H3K27ac

  ChIP-seq peaks of H3K27ac. The dataset includes FASTQ files, BAM files, and analyses of the ChIP-seq peaks of H3K27ac determined using MACS2

  Dataset EGAD00001008964

• The Extracellular RNA Quality Control (exRNAQC) study (phase 2)

  mRNA capture sequencing and small RNA sequencing data (FASTQ files) of the exRNAQC study phase 2 (interaction study)

  Dataset EGAD00001009724

• Hematopoietic differentiation at single-cell resolution in NPM1-mutated AML

  To investigate the relationship between somatic mutations and phenotypic hematologic differentiation at the single-cell level, we used a droplet-based multi-omics single-cell platform on eleven NPM1-mutated AML diagnostic samples. We developed a bioinformatics framework to perform phylogeny-driven genotype correction, that allowed us to study 52 103 single cells. Intra-leukemic genetic heterogeneity was detectable in all patients, including a branched architecture in nine of them, always owing to co-occurring signaling mutations. We identified two groups of NPM1-mutated AML, one characterized by a progenitor immunophenotype and a second one with a predominant monocytic differentiation. We also identified various degrees of intra-leukemic immunophenotype heterogeneity, sometimes associated with strong genetic/phenotype correlations.

  Study EGAS00001006565

• Comparison of the single-cell and single-nucleus hepatic myeloid landscape within decompensated cirrhosis patients

  In-patient comparison of single-cell RNA-sequencing (scRNA-seq) and single-nucleus (snRNA-seq) technologies and accompanying tissue processing protocols on transjugular liver biopsy from decompensated cirrhosis patients (n = 3).

  Study EGAS50000000073

• Single cell sequencing: Capturing the origin and dynamics of chromosomal copy-number heterogeneity

  Study EGAS00001003812

• Human gastrointestinal epithelia of the esophagus, stomach and duodenum resolved at single-cell resolution

  Study EGAS00001004695

• The DNA methylome of cervical cells and risk of ovarian cancer

  Study EGAS00001005045

• Targeted capture sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Targeted capture sequencing for 366 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study and 29 samples from a previously uploaded dataset.

  Dataset EGAD50000001364

• Whole genome sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Whole genome sequencing for 10 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study, and 6 samples from a previously uploaded dataset.

  Dataset EGAD50000001366

• WES for CNV-verified CTCs from 2 patients with metastatic prostate cancer

  This dataset contains 4 paired fastq files sequenced by illumina Novoseq 6000. WES analysis (illumina platform, PE150, 100x coverage) was performed on a pool of CNV-verified CTCs that were enriched using high-throughout microfluidic device from entire leukopak from patients with metastatic prostate cancer (GU-1 and GU-2).

  Dataset EGAD50000001005

• Exome Sequencing for brazilian patients with Idiopathic Collapsing Glomerulopathy

  This dataset contains 2 BAM files sequenced with Illumina NextSeq 500 e NovaSeq 600 and 20 files with variant calling sequenced with Illumina NextSeq 500 e NovaSeq 600.

  Dataset EGAD50000000091

• Illumina whole genome sequencing data for two patients with congenital disease

  BAM files with sequencing reads derived from Illumina whole genome sequencing of two DNA samples from lymphoblastoid cell lines from two patients with congenital disease. Whole genome sequencing was performed using Illumina HiSeq X Ten and samples were prepared using TruSeq library prep.

  Dataset EGAD00001003510

• Whole genome sequencing data to study therapeutic targeting of ependymoma

  This dataset contains whole genome sequencing data from 24 patients. For each patient a tumour and control sample has been sequenced on a Illumina HiSeq2000 instrument in paired-end mode. Up to three lanes per sample have been sequenced resulting in 112 Fastq files.

  Dataset EGAD00001003940

• CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

  Single cell sequencing analysis for Dengue patients using Smart-seq2 and 10X platforms

  Dataset EGAD00001007656

• S:CORT Stratification in COloRecTal cancer

  Colorectal cancer samples will be submitted for Illumina sequencing using a custom capture of 116 genes implicated in colorectal tumourigenesis. Driver mutations will be detected and ultimately correlated with phenotypic data.

  Dataset EGAD00001009760

• Genomic analyses (WES, RNAseq, scRNAseq and scTCRseq) of triple negative breast cancer evolution

  This study explores the evolution of tumor and blood immune microenvironment and related mechanisms that shape breast cancer progression.

  Dataset EGAD50000000117

• Genomic analysis of HPV-positive versus HPV-negative oesophageal adenocarcinoma

  Whole exome sequencing was performed to explore the mutational landscape and potential molecular signature of HPV-positive versus HPV-negative OAC. Four hr-HPV-positive and 8 HPV-negative treatment-naive fresh-frozen OAC tissue specimens and matched normal tissue were analysed to identify somatic genomic mutations

  Dataset EGAD00001001660

• Human tumour and matched-normal single-cell RNAseq

  We profiled 16 high-grade gliomas patient tumour samples by single-cell and single-nuclei RNA-seq and 3 normal-matched single-cell RNA-seq using 10X Chromium 3'. The fastq files are provided.

  Dataset EGAD00001006097

• miRNA and mRNA transcriptome data

  This dataset contains 278 miRNA and 20 mRNA transcriptomes generated as part of the study "miR-374a-5p regulates inflammatory genes and monocyte function in inflammatory bowel disease."

  Dataset EGAD00001008683

• Paired Exome sequencing of Sarcoma tumor and control

  Paired Exome sequencing of Sarcoma tumor and control of 10 samples (5 tumor/control pairs). The sequencing was done on Illumina Hiseq 4000 and Agilent Sureselect V5+UTRs kit.

  Dataset EGAD00001010278

• SPATC1L variants associated with age-related and hereditary hearing loss.

  The dataset contains three BAM files that include SPATC1L variants identified in Italian patients affected by hearing loss (both hereditary and age-related hearing loss). Data have been produced by whole exome sequencing and targeted re-sequencing, using Ion Proton and Ion Torrent PGM platforms respectively.

  Dataset EGAD00001004147

• RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C)

  RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C). Samples used were Whole Blood. Febrile illness controls include children with bacterial and viral infections and healthy controls. This dataset contains samples from patients recruited into the DIAMONDS study.

  Dataset EGAD00001011134

• Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

  RNA seq of iPSC-derived cardiomyocytes cultured in lipid-enriched maturation medium (MM), in MM on nanopattern-surfaces (NP) and under the influence of MM, NP and electrical Stimulation (ES, 2Hz, 14 days). 9 Samples from 3 Independent batches/differentiations of cardiomyocytes from 2 different iPSC-lines (iWTD2.1 and isWT7.22).

  Dataset EGAD00001011289

• RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells.

  RNAseq was performed using 200 ng of total RNA by GATC Biotech. Directional libraries were performed after mRNA selection by polyA selection using UTP method. RNA-seq libraries were sequenced on HiSeq2500 Illumina machine using 100bp paired-end reads. Reads alignment was performed using the STAR aligner (version 2.4.0f1) and human genome hg19 as reference.

  Study EGAS00001004347

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: NOVA1 gain and loss of function systems

  We produced NOVA1 and EGFP over-expression RNA-seq datasets in three healthy control individuals using lentivirus-mediated gene transfer to model NOVA1 gain of function. Additionally, we produced a NOVA1 loss of function RNA-seq dataset by generating iPSC-MN with NOVA1 knock out produced by CRISPR/Cas9 in the CV-B iPSC line.

  Study EGAS00001005881

• Whole genome sequencing of acute erythroid erythroid leukemia

  Briefly, twenty paired tumor and germline DNAs were extracted from patients’ BM and from buccal mucosa, respectively. Samples were subjected to massively parallel sequencing using the HiSeq 2000, HiSeq2500, HiSeq X Ten, and/or NovaSeq 6000 according to the manufacturer’s instructions. Sequencing reads were aligned to NCBI Human Reference Genome Build 37 (hg19) by Burrows−Wheeler Aligner, version 0.7.10, with default parameters (http://bio-bwa.sourceforge.net/). PCR duplicates were eliminated using Picard tools version 1.39 (GATK).

  Dataset EGAD00001008357

• Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort

  Pathogenic germline variants in the protection of telomeres 1 gene (POT1) have been associated with predisposition to a range of tumor types, including melanoma, glioma, leukemia and cardioangiosarcoma. We sequenced all coding exons of the POT1 gene in 2,929 European-descent melanoma cases and 3,298 controls, identifying 43 protein-changing genetic variants. We performed functional studies on each of these variants and explored their possible contribution to disease risk.

  Dataset EGAD00001009848

• Phenotypic Signatures of Circulating Neoantigen-Reactive CD8+ T Cells in Patients with Metastatic Cancers

  Following enrichment of neoantigen-reactive T cells using pHLA tetramers or cell-surface markers, we performed single-cell sequencing (RNA-seq and TCR-seq) of circulating CD8+ T cells from metastatic cancer patient samples (Melanoma, Colorectal, and Breast cancer). In samples from previously studied patients, we identified cells bearing neoantigen-reactive T cell receptors and were able to study their phenotypic program. By studying the circulating neoantigen-reactive T cell program, a gene-signature was derived to identify neoantigen-reactive T cells from blood samples prospectively.

  Study phs003064

• Precursor_lesions__clonal_architecture_and_relapse_in_Wilms_nephroblastoma

  Targeted resequencing at high depth (21 genes, 9 chromosomal regions): at least 4 FFPE samples per case and matched germline DNA: •100 cases with detailed outcome data, including 15 cases with tumour relapse (515 samples)•40 cases with matched pre-chemotherapy biopsies (240 samples)•50 nephrogenic rests matched to above cases (50 samples)We expect a proportion (possibly 10%) of cases to be mutationally silent on the above studies, and propose to subsequently carry out integrated whole-genome, methylome and transcriptome studies on matched frozen tissue from these cases

  Study EGAS00001001422

• Single cell RNA-seq and ATAC-seq of human fetal forebrain tissue, weeks 8 to 11.

  Single cell RNA-seq from 6 and single nuclei ATAC-seq from 3 human fetal tissue samples. Samples from 8 to 11 weeks. Includes a 8.5 weeks samples with matching both ATAC-seq and RNA-seq runs. Data was sequenced using 10X Genomics chromium technology, for scRNA-seq samples belong to v2 and v3.

  Dataset EGAD00001008653

• Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab

  We report herein an extensive exploratory biomarker analysis of refractory tumors taken from pediatric patients prior to receiving atezolizumab monotherapy in the phase 1-2 iMATRIX-atezolizumab trial (NCT02541604). A high percentage of CD8+ T cells and elevated protein levels of programmed cell death ligand 1 (PD-L1) were associated with progression-free survival (PFS). T-cell receptor (TCR) sequencing revealed that diverse infiltrating TCR repertoire at baseline was prognostic. We found no associations between panel-based tumor mutation burden (TMB) or specific genetic aberrations with PFS in this study. Through a pan-cancer gene co-expression network analysis, we developed a novel tumor-agnostic Pediatric Cytotoxicity and Antigen Presentation (PedCAP) signature that was associated with improved PFS in the iMATRIX-atezo study. Our study highlights features of immune response in pediatric cancers when treated with immune checkpoint inhibitors and provides a multi-biomarker pediatric immunogram framework to guide prospective clinical trials in pediatric cancers.

  Study EGAS00001006004

• Contribution of specific cell types to the development of Barrett’s esophagus and carcinoma via germline genetic risk

  We sought to elucidate how individual cell types in Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) contribute to disease development via germline genetic risk.

  Dac EGAC50000000235

• scRNA data of multiple myeloma

  Dataset containing 36 samples of multiple myeloma. The sequencing was always paired and performed on Illumina NextSeq 550 and Illumina NovaSeq 6000.

  Dataset EGAD50000000438

• Methylation array data of thymic epithelial tumors (TC, NET, THYM)

  Methylation microarray data (Illumina 850K) of 52 thymic epithelial tumors. 13 patients with thymoma A and B, 32 thymic carcinoma (TC) and 7 neuroendocrine tumors of the thymus (NET).

  Dataset EGAD00010002355

• Cell line sequencing data

  SmMIP libraries using bulk cell line DNA and DNA mixes were generated in replicates and were sequenced on the NovaSeq SP platform (Illumina)

  Dataset EGAD00001007790

• ATAC Analysis of Treg and Tfh cells

  Treg and Tfh cells (8 Samples)from the same donors was subject to ATAC-seq processing. Paired end fastq-files are supplied.

  Dataset EGAD00001007660

• GBM-Space: Joint Transcriptome and Chromatin Accessibility Profiling of Glioblastoma (10x Genomics - Multiome)

  GBM-Space: Joint Transcriptome and Chromatin Accessibility Profiling of Glioblastoma (10x Genomics - Multiome). Note: 60 new samples were added to the dataset on 2026-05-20.

  Dataset EGAD00001015526

• Spatially resolved single-nucleus RNA sequencing of Choroid Plexus Tumours reveals clinically relevant hypoxia- and stress-driven dedifferentiation programs that sculpt an immunosuppressive and pro-angiogenic microenvironment

  Our study leverages single-nucleus RNA sequencing (~124,500 nuclei) and spatial transcriptomics (~40,650 spots) to dissect the molecular architecture of CPTs. We generated a comprehensive transcriptomic atlas of 45 CPT samples spanning all three methylation groups and a reference cohort of 16 non-neoplastic choroid plexus (ChP) samples, spanning foetal, paediatric and adult specimens. Key discoveries from this investigation include that paediatric B tumorus exhibit a dedifferentiated state and enrichment of stress-related metaprograms, including hypoxia, TGFß signaling, Interferon I signaling and early stress response, that correlate with poor clinical outcome and antagonise multiciliogenesis. On a spatial level, these stress-linked programs co-localise with immunosuppressive, pro-angiogenic microenvironment, suggesting a link between developmental arrest, microenvironmental remodelling and aggressive behaviour.

  Study EGAS50000001617

• Whole-Genome Sequencing Reveals Complex Genomic Features Underlying Anti-CD19 CAR T-Cell Treatment Failure in Lymphoma

  We performed Whole-Genome Sequencing (WGS) on 100 tumor and matched germline samples from 49 CD19-directed chimeric antigen receptor (CAR-19)-treated diffuse large B cell lymphoma (DLBCL) patients. We found that the presence of complex structural variants, APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. BAM files will be available through dbGaP.

  Study phs003023

• Genome-wide analysis of H3K27me3 occupancy and DNA methlytion in pediatric high-grade glioma

  Genome-wide analysis of H3K27me3 occupancy and DNA methylation in K27M-mutant and H3.3-WT primary pediatric high-grade gliomas (pHGGs) as well as pediatric pHGG cell lines. The study aims to elucidate the connection between K27M-induced H3K27me3 reduction and changes in DNA methylation as well as gene expression.

  Dataset EGAD00001000677

• Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

  We investigated 10 female and 14 male SARS-CoV-2 positive children (age range: 0.8 to 18 years). Based on the WHO guidelines, 15 patients were classified as having mild COVID-19, while 7 children were classified as moderate COVID-19 cases. Two children were asymptomatic. 8 female and 10 male SARS-CoV-2 negative children were included as controls (age range: 4 to 16). 12 SARS-CoV-2 positive female and 9 male adults were included ( age range: 27 - 76) together with 13 female and 10 male SARS-CoV-2 negative adult controls (age: 24 - 77). 10 adult COVID-19 patients had mild disease, while 12 had moderate COVID-19. We performed single-cell RNA sequencing experiments.

  Dataset EGAD00001007969

• Genomic variant calling of 32 Chinese SRCCs

  Whole Genome Sequencing has been applied in 32 SRCC patients and the raw data have been subjected to standard procedures. Files with genomic variant calling were obtain at the last step.

  Dataset EGAD00001004045

• ChIP-seq and Hodgkin lymphoma

  ChIP-seq data (H3K4Me3, H3K27Ac histone modifications) of Hodgkin lymphoma cell line L-428. Samples were processed as previously described (Sud et al., 2018). The files are in bam format, aligned to build 37 of the human genome.

  Dataset EGAD00001004322

• sWGS of core biopsies from localized breast cancer patients

  Paired end shallow whole genome sequencing (sWGS) data for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.

  Dataset EGAD00001008397

• Evaluating the immune response in treatment-naive hospitalised patients with influenza and COVID-19 Data Access Committee

  Dac EGAC00001002503

• DAC Unravelling the contribution of HIF pathway and its therapeutic potential in human AML leukemia-initiating cells

  Dac EGAC00001002509

• Aboriginal Genetics and Health Studies based at the Telethon Kids Institute, Perth, Western Australia

  Dac EGAC00001000261

• Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma.

  Study EGAS00001004320

• Extended longitudinal single-cell RNA-seq data from ovarian cancer across multiple treatment phases

  The dataset contains single-cell RNA-seq data of 73 tumor samples high-grade serous carcinoma (HGSC) patients sequenced with Novaseq. The samples were collected at primary, interval, and relapse treatment phases from multiple tissue sites. The files provided are fastq files.

  Dataset EGAD50000001855

• shallow whole genome sequencing BAM files aligned to the human reference genome GRCh38

  We profiled large B-cell lymphoma (LBCL) patient plasma samples with ultra-low-pass (shallow) whole genome sequencing. The DNA sequencing was performed on pre-capture genomic libraries, with an intended mean coverage of at least 0.1X, FASTQ files were cleaned by fastp and mapped to the reference human genome (GRCh38) with bwa.

  Dataset EGAD50000001497

• A thymic ILC1-like progenitor with differentiation potential towards KIR+NKG2A- NK cells

  The dataset contains bulk RNA sequencing data from 12 pediatric thymus samples collected during cardiac surgeries. These samples represent immunologically healthy donors with a mean age of 6 months. The sequencing was performed using Illumina HiSeq4000, and the processed files are available in standard formats such as FASTQ.

  Dataset EGAD50000001120

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 4)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one ETV6::RUNX1 ALL patient (ALLK-132). Novogene's internal method was used in directional library preparation including rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002590