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• Paired RNA-Seq data from 17 samples of different tumors

  Paired RNA sequencing data (21 runs/ 17 samples) of different tumors. The samples were prepared using the Illumina TruSeq stranded mRNA Kit. The sequencing was done on Illumina HiSeq 4000.

  Dataset EGAD00001009706

• WES of germline, nevi, primary and metastatic Cutaneous Melanoma from patient 009 in CASVAC-0401 trial

  Samples: primary cutaneous melanoma (CM) non-associated or distal nevus (A); adjacent or CM-associated nevus (B); Primary-CM (C); and Lymph-Node Metastasis (LN-mts) (D). Whole-exome sequencing (WES) was performed in DNA extracted from the different samples (A-D) paired with the germline reference (G), processed with the Agilent SureSelect All Exon Human V5 Library in an Illumina Hiseq 4000 PE101 platform.

  Dataset EGAD00001009083

• Comparison of the antiviral immune response between individuals of Indian and European origin

  We purified peripheral blood mononuclear cells from individuals living in India (N=10) and the Netherlands (N=10) at baseline and 10-12 weeks after BCG vaccination. We compared chromatin accessibility between the two populations at baseline, as well as gene transcription profiles and cytokine production capacities upon viral stimulation with influenza and SARS-CoV-2

  Dataset EGAD00001009079

• RNA-seq of endometrial organoids from MRKH patients and controls grown under expansion medium or hormonal treatment

  Raw, unfiltered fastq files obtained through RNA-seq of endometrial organoids from MRKH patients and controls. The dataset divides into three parts, depending on the growth conditions of the organoids, ie expansion medium or treated with hormones. Each sample consists of two paired-end fastq files.

  Dataset EGAD00001008453

• Next-generation sequencing data derived from patient single cells or clonal colonies

  The following samples were generated from the patient samples used in the study: - Bulk DNA sequencing specifically targeting mutated sites of interest derived from clonal cell populations (288 monoclonal colonies - 2 replicates). - Targeted Muta-seq method (Patient P342: 2208 cells, Patient HRK: 1066 cells, Patient LAK: 618 cells, Patient P101: 1080 cells) - Smart-seq2 method (Patient P342 - 768 individual cells).

  Dataset EGAD00001006228

• DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  Paired-end DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). Each sample was multiplexed across flowcells and lanes, leading to a total number of 86 FASTQ files.

  Dataset EGAD00001005756

• Genomic Changes in Breast Cancer Among Chinese Women in Hong Kong

  Recently, tumor sequencing and profiling analyses have improved molecular classification and refined existing breast cancer subtypes. However, epidemiologic data are absent in most somatic profiling studies even in extensively studied Western populations. The expansion of genomic studies to understudied populations with the integration of etiologic factors will allow the capture of a much wider range of genetic structure and mutagenic exposures associated with breast cancer risk. We therefore conducted a detailed molecular characterization of paired breast tumor/normal tissues using fresh frozen tissues collected from breast cancer cases in an ongoing breast cancer case-control study in Hong Kong. These analyses included whole genome (WGS)/exome sequencing (WES), targeted DNA panel sequencing, RNA sequencing (RNA-Seq), and genome-wide methylation profiling analyses.

  Study phs001870

• RNA-seq of cultured human hematopoietic stem and progenitor cells from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

  To elucidate the biological pathways altered by sphingolipid modulation with N-(4-hydroxyphenyl) retinamide (4HPR) treatment in human HSPC that may contribute to the restraint in proliferation while promoting persistence of HSC self-renewal as well as determine the mechanism of synergy in enhancement of HSC self-renewal with CB CD34+ agonists UM171 and StemRegenin 1 (SR1), we performed RNA-sequencing (RNA-Seq) of 3 pools of lin-CB cells following 2 or 4 days with DMSO, 4HPR, UM171+SR1 or 3-Factor (4HPR+UM171+SR1). We identified modulation of sphingolipid metabolism regulates self-renewal through activating coordinated stress pathways that coalesce on endoplasmic reticulum stress and autophagy programs.

  Study EGAS00001003756

• Combined – whole blood and skin fibroblasts - transcriptomic analysis in Psoriatic arthritis.

  Whole blood RNA sequencing was performed longitudinally in 27 subjects with PsA at the beginning, one month and six months after treatment and response to therapy was defined at 6 months. As control groups 7 healthy individuals and 9 subjects with rheumatoid arthritis were recruited combined with public RNA-sequencing datasets from patients with psoriasis and systemic lupus erythematous. Differential expression analysis and weighted gene co-expression network analysis were performed to identify gene expression signatures, while deconvolution and flow cytometry to characterize the peripheral blood immune cell profile. RNA sequencing of skin fibroblasts was performed in a subset of affected (n=3) and healthy individuals (n=3) combined with CellChat to identify the blood-skin fibroblasts interaction network.

  Study EGAS00001006288

• FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-Free DNA

  Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from existing datasets, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues of origin directly from plasma whole genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow coverage WGS and whole genome bisulfite sequencing (WGBS) data from both cancer patients and healthy controls.

  Study phs003287

• KIT-dependent and -independent genomic heterogeneity of resistance in gastrointestinal stromal tumors - TORC1/2 inhibition as salvage strategy

  The mutational status of GIST analyzed with a broad sequencing approach (WES, RNAseq)

  Study EGAS00001003405

• McQuillin_Global_WES_Schizophrenia

  Whole Exome Sequencing of Schizophrenia cases and matched controls performed at the Broad Institute on a cohort from UCL, London, UK

  Study EGAS50000000901

• Transcriptomic landscape of C1498 cells

  We characterized the mutations and gene fusion events (at RNA level) of C1498 cells by whole transcriptome sequencing analysis.

  Study EGAS50000001674

• HLA has strongest association with IgA nephropathy in genome-wide analysis

  GWAS study of families with probands with IgA nephropathy from the UK Glomerulonephritis DNA bank

  Study EGAS00000000031

• GermCellTumour

  DNA and RNA sequencing across a number of different germ cell tumours, included mixed components within the same tumour.

  Study EGAS00001003457

• Tumor microenvironment-induced FOXM1 regulates ovarian cancer stemness

  RNAseq from patient-derived primary tumor cells, cultured or not on organotypic cultures mimicking the tumor microenvironment

  Study EGAS50000000355

• Epi_Tax_targeted_sequencing

  Sequencing of 350 cancer genes in BC samples from patients treated with either Epirubicin or Paclitaxel monotherapy in the neoadjuvant setting.

  Study EGAS00001000587

• Multi-omics profiling of PSCCE

  We performed whole-exome sequencing, RNA sequencing and immunohistochemistry profiling of primary small cell carcinomas of the esophagus.

  Study EGAS00001004889

• Detection of MEIS2 inversion using ONT adaptive sequencing

  DNA was extracted from whole blood, and sequenced on a Promethion flow cell. The target region covered chr15:22874354-55370932 (Grch38). The resulting data was aligned to Grch38 using minimap2.

  Dataset EGAD50000000893

• piRNA analysis in human testis

  The dataset comprises RNAseq data of human testiculr tisue of fertile men with full spermatogenesis nd infertile men with biallelic variants in genes of the piRNA pathway.

  Dataset EGAD50000000585

• CMMRD tumors sequencing data

  Whole exome sequencing data from the tumors of individuals with constitutional mismatch repair deficiency. These are 16 tumors from the bigger study of 41 tumors in total (from 17 individuals in total).

  Dataset EGAD50000000113

• AI

  Allelic imbalance (AI) region calls: start and end positions and the measured mBAF and LRR mean of each region after the BAF segmentation algorithm. Software: Illumina GenomeStudio;PennCNV v. 1.0.4;BAF segmentation v1.2.0.

  Dataset EGAD00010001926

• The Extracellular RNA Quality Control (exRNAQC) study (phase 1)

  mRNA capture sequencing and small RNA sequencing data (FASTQ files) of the exRNAQC study phase 1.

  Dataset EGAD00001007697

• CBB post-mortem hippocampal short-RNA-seq

  Short RNA sequencing of post-mortem human hippocampi from the Calgary Brain Bank. The dataset includes patients with Alzheimer's disease (AD) and healthy control individuals (Ctrl).

  Dataset EGAD00001006886

• Analysis of the Patient derived cells that model the intratumoral heterogeneity of hypermutated IDH1 mutant glioma

  Dataset contains paired-end Whole Exome sequencing data from 2 glioma patients (1 oligodendroglioma and 1 astrocytoma) , derived cultured cells, and derived murine xenografts.

  Dataset EGAD00001006340