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• Raw molecular data for "Subclonal immune evasion in non-small cell lung cancer"

  Whole exome, RNA sequencing and TCR sequencing of organoid samples derived from TRACERx patients. The dataset also includes whole exome sequencing from the tumour samples from which the organoids were generated, as well as whole exome sequencing from PDX derived from said tumours.

  Dataset EGAD00001015537

• Deep exome sequencing

  Bam files from deep exome sequencing of blood DNA samples from five TET2 mutation carriers (Ly1, Ly2, Ly9, Ly11, Ly14) and three wild-type family members (Ly8, Ly10, Ly13) extracted at multiple time points. Library preparations were performed with SeqCap EZ Exome v3 (Roche, Switzerland) using six different index primers per sample for which paired-end Illumina sequencing was done with 75bp read length and HiSeq4000 sequencer. After alignment (bwa version 0.7.12), base recalibration (GATK 3.5), realignment around indels (GATK 3.5) and duplicate removal (MarkDuplicates; Picard Tools version 1.79), data from libraries with six different indexes were merged.

  Dataset EGAD00001004780

• Finding structural variation from the patient-derived xenografts of pediatric T-cell leukemia at the single-cell level

  In this study, we aimed to identify somatic structural variation of T-cell acute lymphoblastic leukemias (T-ALLs_ from patient-derived xenografts (PDX) at the single-cell level. For this purpose, we performed strand-specific single-cell sequencing of PDX-derived T-ALL relapse samples from two juvenile patients (P1, P33). To validate structural variation detected via scTRIP, we profiled whole exome sequencing (WES) data from P33 (samples taken during initial disease, remission, relapse), and mate-pair sequencing data from P1 (relapse).

  Dataset EGAD00001004499

• Single-cell expression of Hodgkin and Reed-Sternberg (HRS) cell

  Hybrid capture sequencing was performed to 3 purified Hodgkin and Reed-Sternberg (HRS) cell samples. In brief, Probes for 177 genes were designed and synthesized by Twist Bioscience. Hybridization capture of DNA libraries was performed using Twist Hybridization and Wash Kit (Twist Bioscience). The captured library was measured using Agilent Bioanalyzer High Sensitivity chip and Qubit dsDNA HS Assay Kit and run on Illumina Nextseq550. The BAM files were generated from the raw sequencing data using Cell Ranger (v6.0.2) mkfastq and count commands

  Dataset EGAD00001010892

• Bulk RNA sequencing of SARC PDOs and UroCa PDOs.

  This dataset contains raw FASTQ files from bulk RNA sequencing of SarBC-01 organoids at different passages (Passage 6, Pssage 19, Passage 59), UroBC-01 organoids (Passage 70), UroBC-16 organoids (Passage 19) and UroBC-22 organoids (Passage 8). RNA was isolated using the Quick-DNA/RNA Miniprep kit (Zymo Research, Irvine, CA, USA, D7001) and subjected to bulk RNA sequencing. TruSeq Stranded mRNA kit (Illumina, 20020594) was used for the library preparation according to manufacturer’s guidelines. Sequencing was performed on Illumina NovaSeq 6000 using paired-end 100-bp reads.

  Dataset EGAD00001011156

• Glioma International Case Control Study (GICC)

  The main goals of the GICC Study were: 1) to identify novel genetic risk variants for glioma, as well as validate variants implicated by previous genome-wide association studies of glioma; and 2) to explore biologically relevant gene-gene and gene-environment interactions in glioma susceptibility. The GICC Study includes participants from the following centers: Brigham and Women's Hospital (Boston, Massachusetts), Case Western Reserve University (Cleveland, Ohio), Columbia University (New York, New York), the Danish Cancer Society Research Centre (Copenhagen, Denmark), Duke University (Durham, North Carolina), the University of Texas MD Anderson Cancer Center (Houston, Texas), Memorial Sloan Kettering Cancer Center (New York, New York), the Mayo Clinic (Rochester, Minnesota), NorthShore HealthSystem (Chicago, Illinois), Umea University (Umea, Sweden), the University of California, San Francisco (San Francisco, California), the University of Southern California (Los Angeles, California), and the Institute of Cancer Research (London, United Kingdom).

  Study phs001319

• The Role of ZEB2 during Human Neural Crest Cell Formation

  This study examined the role of ZEB2 during human neural crest cell formation. Human neural crest cells were differentiated from WiCell H1 human embryonic stem cells (WA01). Genome-wide transcriptional analysis (RNA-seq) was performed at day-3 and day-5 of human neural crest cell formation following siRNA knockdown of ZEB2 and using an N-terminal ZEB2 mutant H1 human embryonic stem cell line generated using CRISPR genome editing. RNA-seq was also performed on edited and unedited H1 human embryonic stem cells. ATAC-seq analysis was performed at day-3 and day-5 human neural crest differentiated from the N-terminal ZEB2 mutant embryonic stem cell line. Together, these data reveal the regulatory role of ZEB2 in the human neural crest gene regulatory network. We provide raw sequencing files for all RNA-seq and ATAC-seq samples.

  Study phs002701

• MuTHER_adipose_tissue_small_RNA_expression

  We investigate the naturally occurring variation of small RNA expression in conjunction with genetic and gene expression variation. We shall assess the variation in subabdominal fat tissue small RNA levels in 168 unrelated MuTHER individuals. Using gene expression data from the same samples, we can survey how much the small RNA expression contributes to the variance in gene expression profiles. We can also take advantage of the high density genotyping data on these samples to identify genetic associations of small RNA expression levels, and the downstream effect of the genetic variants in small RNA sequence. Previous small RNA sequencing efforts have also extended the repertoire of small RNAs, and we hope to potentially find additional small RNAs active in adipose tissue biology. Altogether, the project should provide an exciting view into small RNA biology in humans, and lead to development of new methodology for analysis of molecular phenotype data.

  Study EGAS00001000212

• RNAseq of whole blood in 359 idiopathic pulmonary arterial hypertension patients reveals biological heterogeneity

  Patients with idiopathic, heritable, or drug-induced pulmonary arterial hypertension (referred to throughout as PAH) were recruited from expert centers across the UK as part of the PAH Cohort study (www.ipahcohort.com). In each case, diagnosis was confirmed by right heart catheterization following established international guidelines, which remained unchanged for the duration of this study. Healthy volunteers were recruited at the same centers and samples processed using the same standard operating procedure at all sites. All individuals gave written, informed consent with local ethical committee approval. Whole blood (3 ml) was collected in Tempus Blood RNA Tubes, and RNAseq was performed using established Illumina methodologies (see online supplement for further details).

  Dataset EGAD00001007981

• WGS files for Genomic Landscape ALL paper

  WGS files for Genomic Landscape ALL paper titled "The genomic landscape of pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001008600

• The immunological characterization of expanded tumor-infiltrating lymphocytes in renal cell carcinoma patients

  In this study, we comprehensively characterized the non-expanded and expanded tumor-infiltrating lymphocytes (TILs) from treatment-naïve RCC patients, as well as the corresponding “young” TILs (pre-REP TILs) and “rapidly expanded” TILs (REP TILs) following a clinical-grade TIL production protocol. From our scRNA+TCRαβ-seq and TCRβ-seq analyses, we show that the REP protocol preferentially favors the expansion CD4+ T-cells that originate from small T-cell clones in the tumor microenvironment (TME), indicating that the large, exhausted T-cell clones in the tumor do not expand during the protocol. We further identified RCC-associated TCR motifs that were validated in multiple TCRαβ-seq and scRNA+TCRαβ-seq datasets, as well as quantified the RCC-associated TCRs from the REP protocol. Overall, the T-cells carrying the RCC-associated TCRs remained high in the tumors and corresponding pre-REP TILs, but the frequency was reduced in the REP TILs. Furthermore, the overall anti-viral TCRs remained low throughout the REP protocol. Our results provide an in-depth understanding of the origin, phenotype, and specificity of the TCRs in RCC TILs.

  Study EGAS00001006952

• Covid19 Transcriptomic Data analysis in Irish Population

  The Samples were collected from Saint James's Hospital, Dublin and after informed consent. RNA-Sequencing library preparation was performed using the Illumina TruSeq Stranded Total RNA Library Prep Globin kit (20020612) with an input amount of 100 – 1000 ng. Library preparation was automated and processed using a Hamilton NGS Star. Library quality was assessed using the Roche KAPA Library Quantification Kit (7960298001) and GX Caliper HS Assay (CLS760672, 760517), run on Roche Lightcycler 480 II and Perkin Elmer LabChip GX Touch analyser respectively. Libraries were pooled and sequenced (75bp PE) on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 S2 Reagent Kit v1.5 (20028314) targeting 50M paired reads. Raw data (BCL format) were demultiplexed and converted to FASTQ format using BCL2FastQ (Illumina). Adapters were trimmed using Skewer (PMID: 24925680) and QC assessed using FASTQC. STAR (PMID: 23104886) was used to align reads to the reference genome (GRCh38/hg38) as well as to the transcriptome (GENCODE v. 25). Quality of the RNA alignment was assessed using Picard QC. Gene and isoform quantification was performed using RSEM (PMID: 21816040). The study shares expression data (gene.results) and chimeric.junction.out.

  Study EGAS00001007116

• Convergent somatic mutations in effectors of insulin signalling in chronic liver disease

  Chronic liver disease is associated with metabolic dysregulation, liver failure and hepatocellular carcinoma. We analysed somatic mutations from 1202 genomes across 32 liver samples, including normal controls, alcohol-related and non-alcoholic fatty liver disease. Five of 27 patients with liver disease carried hotspot driver mutations in FOXO1, the major transcription factor downstream of insulin signalling. FOXO1 mutations were independently acquired by up to 5 distinct clones within the same patient’s sample, and impaired insulin-mediated nuclear export of FOXO1. GPAM, which produces storage triacylglycerol from dietary calories, also had significant excess of mutations, similarly exhibiting convergent evolution within biopsies. Telomeres were shorter in diseased than normal liver, with attrition more pronounced in larger clones. Multiple independent acquisitions of drivers within one small liver sample imply that such mutations could affect hundreds of grams of tissue across the whole organ, potentially contributing to systemic metabolic dysfunction.

  Dataset EGAD00001006255

• Genetics causes of male infertility in 185 patient-parent trios from Netherlands and UK

  The dataset is composed by the raw and processed sequencing data generated from 185 Patients affected by azoospermia or severe oligozoospermia recruited from the Netherlands and the UK.

  Dataset EGAD00001007862

• The Dutch Microbiome Project Batch 2

  The Dutch Microbiome Project (DMP) data includes shotgun metagenomic sequencing of faecal samples 8,208 Dutch individuals. Paired-end sequencing was performed using Illumina HiSeq 2000 platform. Data is archived in two batches to facilitate easier data access and upload to EGA. Batch 2 of DMP includes ~400 samples.

  Dataset EGAD00001007501

• OV04 chemo prediction

  Predicting resistance to chemotherapy using chromosomal instability signatures Joe Sneath Thompson1,2,*, Laura Madrid2,*, Barbara Hernando1,*, Carolin M. Sauer3, Maria Vias3, Maria Escobar-Rey1,2, Wing-Kit Leung2,3, Diego Garcia-Lopez2, Jamie Huckstep3, Magdalena Sekowska3, Karen Hosking4,5, Mercedes Jimenez-Linan5,6, Marika A. V. Reinius3,5,6, Abhipsa Roy2, Omar Abdulle2, Justina Pangonyte3, Harry Dobson2, Amy Cullen2,3, Dilrini De Silva2, David Gómez-Sánchez1,7, Marina Torres1, Ángel Fernández-Sanromán1, Deborah Sanders3, Filipe Correia Martins3,5,6, Ionut-Gabriel Funingana3,4,5, Giovanni Codacci-Pisanelli3,4,8, Miguel Quintela-Fandino1, Florian Markowetz2,3,4, Jason Yip2, James D. Brenton2,3,4,5,6, Anna M. Piskorz#,2,3, Geoff Macintyre#,1,2 1 Spanish National Cancer Research Centre (CNIO), Madrid, Spain 2 Tailor Bio Ltd, Cambridge, UK 3 Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK 4 Department of Oncology, University of Cambridge, Cambridge, UK 5 Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK 6 Cancer Research UK Major Centre - Cambridge, University of Cambridge, Cambridge, UK 7 H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain 8 University of Rome "la Sapienza", Rome, Italy

  Dac EGAC50000000612

• Whole Exome Sequencing analysis of three tumor biopsies from a LUAD patient

  Whole Exome Sequencing (WES) analysis was performed on three distinct tumor biopsies collected at different time points, along with their matched germline non-tumor sample, from the same LUAD patient. DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions and quantified using the Qubit Fluorometer assay (Life Technologies, Carlsbad, CA). To minimize FFPE-related sequencing artifacts (e.g., C:G > T:A transitions), the extracted DNA was treated with the DNA repair enzyme Uracil-DNA-Glycosylase (UDG) following the manufacturer’s protocol (New England Biolabs, Ipswich, MA). Whole-exome capture was performed with the Twist Human Core Exome + RefSeq + Mito-Panel kit (Twist Bioscience), in accordance with the manufacturer’s guidelines. Sequencing generated paired-end 100-bp reads on the Illumina NovaSeq 6000 platform. The resulting reads were aligned to the reference human genome (GRCh38) using the Burrows-Wheeler Aligner (BWA, v0.7.12).

  Dataset EGAD50000001198

• A 3D genome atlas of breast cancer progression (BRCA3D)

  In this study, we aimed to understand how the 3D genome changes during breast cancer development and progression, in situ. Towards this goal, we collected cells from patient biopsies and performed Hi-C on four types of biopsies representing different stages of disease progression: healthy mammary tissue, primary breast tumours, liver metastasis and malignant pleural effusions. We survey the changes in the 3D genomes at the level of structural variation, compartments and TADs, as well as ERα associated distal interactions.

  Study EGAS50000000444

• Plasma cfDNA dsDNA and ssDNA shallow whole genome and exome sequencing data

  This dataset includes fastq files from sWGS and exome sequencing data derived from dsDNA and ssDNA libraries of plasma cfDNA samples extracted by a column- or bead-based DNA extraction method

  Dataset EGAD00001007019

• RNA-seq of high-grade serous ovarian cancer in long-term survivors (MOCOG study)

  RNA-seq dataset of high-grade serous ovarian cancer (HGSC) tumours from long-term survivors performed as part of the Multidisciplinary Ovarian Cancer Outcomes Group (MOCOG) study. The dataset includes fastq files from 56 HGSC tumours (53 primary tumours and 3 recurrent tumours) from 53 long-term survivor patients. Libraries were generated using the Illumina Stranded mRNA Prep and 150 bp paired-end sequencing was performed to a minimum of 100 million reads on Illumina NovaSeq 6000 instruments.

  Dataset EGAD00001008537

• RNA-seq datatset of primary human thymocyte subsets

  FASTQ-files of RNA-seq experiments of 8 primary human thymocyte subsets, isolated by flow-cytometry (FACS) from neonatal thymus biopsies. All samples were sorted to be negative for the expression of the lineage surface markers CD11c, CD19, CD56, CD141 and CD303 and additionally had the following surface phenotypes: DN1 (CD4-CD8-CD7+CD1a-CD161-CD38-); DN2 (CD4-CD8-CD7+CD1a-CD161-CD38+CD3-TCRab-); DN3 (CD4-CD8-CD7+CD1a+); ISP (CD4+CD8-CD3-TCRab-CD1a+); DPE (CD4+CD8+TCRab-CD69-); DPL (CD4+CD8+TCRab+CD69+); SP4 (CD4+CD8-); SP8 (CD4-CD8+). Samples were sorted from 2-4 pediatric patients undergoing heart surgery.

  Dataset EGAD50000001599

• Dataset of 2485 CD8 T cells from non-muscle-invasive bladder cancer patients in context of BCG treatment

  FASTQ files from scRNAseq (smartseq2 protocol) from 2485 CD8 T cells from 4 non-muscle-invasive bladder cancer patients who received BCG treatment (induction treatment of 6 weekly instillations). Concerning the 'phenotype' column in metadata : pre-treatment samples include tumor samples ('Tumor') and normal adjacent bladder tissue ('Extratumor'). For post-treatment samples : no residual tumor was found in the bladder of the 4 patients after the BCG treatment . The post-treatment samples with 'Tumor' as phenotype denote samples from macroscopically suspect zones, but with microscopically no tumor detected.

  Dataset EGAD50000002007

• Bulk RNA and ATACseq of 2 XLP patients and 5-6 HD

  The dataset contains five samples from P1, one pre-HSCT and four post-HSCT, one sample from P2 and 5-6 HD. RNAseq reads were processed using the LUMC BIOWDL RNAseq pipeline v5.0.0 (https://github.com/biowdl/RNA-seq). Genes with log2CPM≥1 in at least 10% of all samples were retained for downstream analysis. Differential gene expression analysis was performed using the dgeAnalysis R-Shiny application (https://github.com/LUMC/dgeAnalysis/tree/v1.4.4). ATACseq reads were processed using the LUMC BIOWDL Chipseq pipeline 1.0.0-dev (https://github.com/biowdl/ChIP-seq).

  Dataset EGAD50000002072

• Dataset of scRNAseq from 56 CRC, treatment-naive and post-chemotherapy

  The dataset includes FASTQ source files of scRNA-seq for 56 CRC patients, sequenced with Illumina 10x platform. All patients were diagnosed with colorectal cancer between 2014 and 2022 at the Gustave Roussy Institute. Cohort includes 32 samples from untreated patients and 24 samples from patients who received chemotherapy. Chemotherapy included FOLFOX or FOLFIRI as first line, in some cases in combination with anti-VEGF or anti-EGRF drugs (avastin, bevacizumab or cetuximab) as the second and third lines. The post-treatment cohort included 18 responders (partial response, stable disease and complete response) and 6 progressors (progressive disease).

  Dataset EGAD50000001218

• Single-nuclei multiomic analysis of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  Datasets consists of 12 samples of nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. 6 single nuclei (RNA-ATAC) samples of XMAS protocol with cells collected at days 0,11,16,28,42 and 56 after differentiation. 3 snRNA-seq samples from AMS protocol of cells collected at days 14,16 and 28 after differentiation and 3 snRNA-seq samples with AMS protocol until day 14 grafted and grafts processed after 5 months grafting.

  Dataset EGAD50000002054

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the feature of age-associated helper T (ThA) cells and its contribution to autoimmune diseases, single-cell RNA-sequencing analysis of peripheral blood CD4+ T cells from healthy control, CD4+ T cells in muscles and bronchoalveolar lavage fluid (BALF) from patients with idiopathic inflammatory myopathy were conducted.

  Study JGAS000648

• Identification of cell type differences in FOXN1 mutation carriers by scRNA-seq

  scRNA-seq was performed on the BD Rhapsody platform. CD45+ lymphocytes from two FOXN1het patients and one cord blood sample as control were sorted from frozen cryopreserved samples. The samples were split and each sample was stained with 4 Sampletag antibodies before Abseq staining with the BD Immune Discovery panel and 6 additional antibodies was performed to better classify immune cell subsets. The sorted and stained populations were pooled before loading onto the BD Rhapsody cartridge. The manufacturer's protocol was followed for library construction and samples were sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD50000001708

• Methylation analysis for plasma DNA of patients with organ transplantation

  We developed Genetic-Epigenetic Tissue Mapping (GETMap) to determine the tissue composition of plasma DNA carrying genetic variants not present in the constitutional genome through comparing their methylation profiles with relevant tissues. We validated this approach by showing that, in pregnant women, circulating DNA carrying fetal-specific alleles was entirely placenta-derived.

  Study EGAS00001004788

• Donor InSight III study: Participants typed during UK Biobank version 2 array development phase

  The Donor InSight III study, undertaken by Sanquin research, recruited 3,046 Dutch blood donors between 2015 and 2016. The purpose of the study was to gain more insight into characteristics of donors, their motivations and health. All participants were at the time of recruitment active blood donors. Genotyping data was produced using the Thermo Fisher Scientific Axiom Genotyping platform. The UK Biobank version 2 array design was used, content on this array has been added to allow for accurate DNA based identification of human blood group antigens.

  Dataset EGAD00001005026

• RNA sequencing of peripheral blood samples from 17 Greenlanders

  The data contain whole deep RNA sequencing of leukocytes from 17 Greenlanders. RNA was purified from peripheral blood with the PAXGene Blood miRNA Kit (Qiagen). The RNA sequencing library was prepared following the instructions of the TruSeq RNA Sample Prep Kit v2 (Illumina). For mRNA isolation and fragmentation 200 ng of total RNA was purified by oligo-dT beads. The qualified libraries were amplified on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3–cBot–HS, Illumina). The amplified flow cell was sequenced paired-end on the HiSeq 4000 System (TruSeq SBS KIT-HS V3, Illumina).

  Dataset EGAD00001003814

• Single MII oocyte mRNA expression from women

  This dataset contains 14 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from ovarian tissue from unstimulated patients undergoing fertility preservation treatments due to cancer diagnoses, which did not influence ovarian function. Cumulus-oocyte-complexes were matured in vitro according Gruhn et al (Science 365: 1466-1469) and short term flash frozen prior to lysis, RNA extraction, full length cDNA preparation and amplification using the Ultra-low-input SMART-Seq2 v4 kit from Takara Clonetech. Further, these cDNA were used to prepare libraries for sequencing according the Nextera XT DNA library preparation kit from Illumina

  Dataset EGAD00001005971

• Leukemia WGS data

  Whole-genome sequencing data from 38 leukemia patients and 12 leukemia cell lines; Containing 100 fastq files; Two files for each sample.

  Dataset EGAD00001008659

• Dataset for hepatopancreaticobiliary_malignancy-EXON

  Rare cancer sequencing data of 162 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008883

• Dataset for hematopoietic_malignancy-EXON

  Rare cancer sequencing data of 91 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008882

• Dataset for urologic_cancer-EXON

  Rare cancer sequencing data of 112 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008904

• CITEseq data

  CITEseq data of CLL patients receiving VEN treatment for resistance study

  Dataset EGAD00001008366

• Dataset for negative_WGS

  WES/WGS sequencing data of 239 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009279

• CCMA-WGSraw

  This dataset has the mapped bam files from WGS for the cancer models in CCMA.

  Dataset EGAD00001010035

• Whole Genome-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015712

• Gut metagenome from Estonian Microbiome Cohort

  Stool samples were collected from 2,509 Estonian Biobank participants. The shotgun metagenomic paired-end sequencing was performed by Novogene Bioinformatics Technology Co., Ltd. using the Illumina NovaSeq6000 platform, resulting in 4.62 ± 0.44 Gb of data per sample (insert size, 350 bp; read length, 2 × 250 bp). A total of 2,513 samples belonging to 2,509 individuals were sequenced, including 4 biological replicates from one individual. First, the reads were trimmed for quality and adapter sequences. The host reads that aligned to the human genome were removed using SOAP2.21 (parameters: -s 135 -l 30 -v 7 -m 200 -x 400).

  Dataset EGAD00001008448

• Myeloma Genome Project Targeted Panel Validation dataset

  372 samples consisting of 185 patient paired CD138+ tumor and non-involved DNA pairs, plus 5 Horizon Diagnostic known mutation standards (HD). Samples were processed using the KAPA HyperCap protocol and hybridized onto a targeted panel for multiple myeloma and associated diseases. Reference Sudha et al Clinical Cancer Research, 2022.

  Dataset EGAD00001008689

• Further details about data access are available at KNIH DAC.

  Dac EGAC00001000487

• Synchronous patterning of hiPSC-derived CNS progenitors generates comprehensive axial spinal cord organoids (CASCOs) containing diverse motor neuron population

  Dataset includes scRNA-sequencing data of cells isolated by dissociation of ~20 BJ WT day 20 hiPSC-derived MN embryoid bodies generated in ULA 96w plates following the protocol described in Rodriguez-Muela et al., JCI 2018). Droplet-based scRNA-seq was performed using 10X Genomics scRNA-sequencing was performed using 10X Genomics Chromium Single Cell Kit v3. The resulting sequencing reads were processed as described in Buchner et al 2024. Analysis of the count matrices was performed using the R toolkit for single cell genomics, Seurat v5.1.0, with R v3.3.3 “Angel Food Cake.”

  Dataset EGAD50000001301

• TSO500 sequencing of ovarian tumour samples

  This dataset consists of 8 ovarian cancer DNA sample libraries prepared using the Illumina TruSight Oncology 500 Kit (Illumina, cat no. 20076480) following the manufacturer's protocol. Library quality and quantity were assessed with High Sensitivity/D5000 Screentape Assay (Agilent Technologies, cat no. 5067-5592) on 4150/4200 Tapestation Quant-IT/Qubit dsDNA HS (Qiagen, cat no. Q32851) assay according to the supplier’s recommendations. Libraries were then pooled together in equal ratios and sequenced using PE-150bp mode on NovaSeq S1 flow cell 300 cycles kit (Illumina, 20028317) or S4 flow cell 300 cycles kit (Illumina, 20028312) aiming for 100 million reads per sample. The dataset contains sequence reads in fastq file format.

  Dataset EGAD50000001451

• Sequence data to study genomic CNVs that drive apoptotic resistance and relapses on immune checkpoint inhibitors

  The dataset consists of bulk whole exome sequencing (WES) and whole genome sequencing (WGS) data from baseline and disease-progressed tumors after immune checkpoint inhibitor (ICI) treatment, derived from patients, human cell lines, and mouse models. Whole exome sequencing includes 17 clinical cases and one human cell line model with parental and acquired resistant cell lines (n = 5). Whole genome sequencing encompasses the YUMMER mouse model, including vehicle-treated controls (n = 2) and acquired resistant tumors (n = 3). The sequence reads have been aligned to hg19 and mm9 reference genomes, with mapped files (BAM) made available for analysis.

  Dataset EGAD50000001537

• 10X CD4 auto-antigens

  Ex vivo CD4 T-cells from 4 donors were stimulated with antigen-coupled beads to aCD3, ABD, EBNA1, ANO2 or CRYAB and the LiveCD3+CD4+CFSEdim cells were sorted by flow cytometry. Cells were labelled with barcoded antibodies to identify the original stimulus. All stimulations from each donor were pooled into four reactions, i.e. one reaction per donor. Libraries were assembled with the 10X Chromium Next GEM Single Cell 5’ Kit for TCR and transcriptome with feature barcodes. Dataset contains raw fastq reads as well as supplementary information needed to link fastq files to modality, i.e. gene-expression, protein or VDJ, and includes supplementary information to de-multiplex the reactions by stimulation condition.

  Dataset EGAD50000002201

• Characterizing the immune and genome landscapes for osteosarcoma

  Osteosarcoma have heavily rearranged genomes and moderate tumor mutation burden, which suggests that the patients may express neoantigens that could be targeted by immune cells. To characterize the immunogenomic landscape of this disease, we performed genome, transcriptome, immune and proteomic profiling of 48 patients comprised largely of relapsed and metastatic cases from both pediatric and adult patients.

  Study EGAS00001003247

• McGill EMC Community projects Release 7 for cell line "hTERT RPE1"

  Complete reference epigenome (as defined by IHEC) of normal hTERT RPE1 cell line as well as hTERT RPE1 cell lines engineered to express EPC1-PHF1 and JAZF1-SUZ12 fusion proteins, found in Endometrial Stromal Sarcoma.

  Dataset EGAD00001007680

• Characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

  RNA was extracted from eight diagnostic ETV6-RUNX1 positive acute lymphoblastic leukemia samples collected in PAXgene blood RNA tubes using PAXgene Blood RNA kit (cat #762174, Qiagen GmbH, Hilden, Germany), following the version 2 instructions for manual purification. Samples were processed with Globin-Zero Gold rRNA Removal Kit (Illumina) and directional libraries were prepared using NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs). The library preparation and paired end (150 bp) sequencing were performed by Novogene (HK) Company Limited (Hong Kong, China) using Illumina Novaseq 6000 aiming at 70 million read pairs per sample.

  Dataset EGAD00001006406

• Dataset for HCPlus_WGS

  WES/WGS sequencing data of 337 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009274

• WGS data for HGSC patient derived organoids and matching tumor and normal samples (Wennerberg)

  Sequencing data of 10 high-grade serous carcinoma (HGSC) patients (58 samples including blood derived normal samples as germline controls, fresh frozen tissue samples as tissue controls and organoids) sequenced with HiSeq X Ten / BGISEQ-500 / MGISEQ-2000.

  Dataset EGAD00001010019

• 76 cancer and normal whole genomes from eleven SI-NET patients

  This dataset comprises of 76 cancer and normal whole genomes obtained from 11 SI-NET patients, in the form of two fastq files (forward and reverse reads) for each genome containing sequences generated by Illumina NovaSeq 6000 system.

  Dataset EGAD00001006161

• Organoid Derivation Project - GRCh38 - WGS (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011093

• Tandem DNA Repeats Activate hTERT Gene Transcription

  Multiple independent sequence variants of the hTERT locus have been associated with telomere length and cancer risks in genome-wide association studies. Here, we identified an intronic variable number tandem repeat, VNTR2-1, as an enhancer-like element, which activated hTERT transcription in a cell and chromatin-dependent manner. VNTR2-1, consisting of 42-bp repeats with an array of E-boxes, cooperated with the proximal promoter in hTERT regulation by bHLH transcription factors and maintained hTERT expression during embryonic stem cell differentiation. Genomic deletion of VNTR2-1 in MelJuSo melanoma cells markedly reduced hTERT transcription, leading to telomere shortening, cellular senescence, and impairment of xenograft tumor growth. Interestingly, VNTR2-1 lengths varied widely in human populations.  To assess the genetic polymorphism of VNTR2-1 in human populations, we analyzed genomic DNA samples of Caucasian Americans and African Americans enrolled in the Georgia Centenarian Study.  VNTR2-1 in these genomic DNA samples were PCR amplified and subjected to sequencing analysis usinb the PacBio® SMRT method. The result showed that all VNTR2-1 alleles in Caucasian Americans contained 76 or more 42-bp repeats, whereas 32% of VNTR2-1 alleles in African Americans had fewer than 76 repeats.  

  Study phs002428

• Single cell transcriptomic landscape of pediatric B-cell acute lymphoblastic leukemia: dissection of transcriptional heterogeneity and B-cell developmental state

  Introduction: Genomic analyses of bulk ALL samples have improved our understanding of the genetic basis and risk stratification of B-ALL, but do not directly examine intratumor heterogeneity or enable inference of leukemia developmental state and cell of origin. Methods: We profiled 89 B-ALL samples by single-cell RNA-seq (scRNA-seq) (10X Genomics 5’v2) and compared them to a scRNA-seq reference map of normal human B-cell development. Results: Analysis of heterogeneity of inferred DNA copy number alterations at single cell level showed that aneuploid ALL with near haploidy and hyperdiploid harbor chromosomal losses or gains in all blasts, consistent with early, synchronous origin rather than sequential accumulation. Intra-sample heterogeneity was driven by five gene expression signatures: cell cycle, metabolism, differentiation, inflammation, refining leukemic subtyping. An atlas of B cell development was established to map B-ALL samples to specific developmental states. Hyperdiploid samples resembled pro-B cells, while MEF2D-r and TCF3::PBX1 showed high pre-B abundance. Patients with high early lymphoid abundance had poorer outcomes. Conclusions: Understanding variation in transcriptional programs and developmental states of B-ALL blasts by sc transcriptome refines existing clinical and genomic classifications and provides novel prognostic markers.

  Study EGAS00001007512

• Genetic drivers of epigenetic and transcriptional variation of human immune responses to infection (RNA-seq, ATAC-seq and ChIPmentation)

  RNA-seq, ATAC-seq and ChIPmentation data from monocyte-derived macrophages that were infected with Influenza A virus strain PR8WT, or a matching non-infected control.

  Dataset EGAD00001008422

• Somatic Mutations in 3,929 HPV-Positive Exfoliated Cervical Cell Samples

  We investigated the detection, timing, and HPV type specificity of cervical somatic hotspot mutations (i.e., previously reported cancer driver mutations) in 3,929 HPV-positive exfoliated cervical cell samples from individuals undergoing routine cervical screening in the U.S. using deep-targeted sequencing of 20 candidate genes. Our study included samples from 3,351 women with the following infection outcomes: 1,478 HPV16-, HPV18- and/or HPV45-positive controls (i.e., HPV infections that did not progress to precancer and/or subsequently cleared), 1,712 cervical precancers, and 161 invasive cervical cancers. We utilized residual exfoliated cervical cell samples from women routinely screened for cervical cancer precursors at Kaiser Permanente Northern California (KPNC) as part of the prospective KPNC-NCI HPV Persistence and Progression (PaP) cohort. We included 3,929 samples collected from these 3,351 women, including 974 serial sample from 396 women collected prior to their most recent screening visit to evaluate somatic hotspot mutation detection prior to diagnosis.

  Study phs003691

• Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples

  This study aims at assessing whether FFPE material can be used for cohort analysis. To this end, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE whole genome sequences samples extracted from the same metastatic prostate tumor. Four variant callers were used to call somatic variants on both the FF and the FFPE samples. An heuristic was developed to maximize the overlap between the FF and its FFPE counterparts. Then, the extent to which intra-tumor heterogeneity explains discrepancies in variants called between the FF and the FFPE samples was assessed by comparing the clonal and subclonal somatic variants. This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.

  Study EGAS00001004456

• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

  In many areas of oncology, we lack sensitive tools to track low burden disease. While cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low disease burden monitoring through the prevailing deep targeted sequencing paradigm. We reasoned that breadth may supplant depth of sequencing to overcome the barrier of cfDNA abundance. Whole genome sequencing (WGS) of cfDNA allowed ultra-sensitive detection, capitalizing on the cumulative signal of thousands of somatic mutations observed in solid malignancies, with TF detection sensitivity as low as 10-5. The WGS approach enabled dynamic tumor burden tracking and post-operative residual disease detection, associated with adverse outcome. Thus, we present an orthogonal framework for cfDNA cancer monitoring via genome wide mutational integration, enabling ultra-sensitive detection, overcoming the limitation of cfDNA abundance, and empowering treatment optimization in low-disease burden oncology care

  Study EGAS00001004406

• RNA sequencing data for primary and recurrent ovarian granulosa cell tumors

  RNA sequencing dataset for primary and recurrent ovarian granulosa cell tumors consists of 24 .bam files with aligned reads, including 8 primary and 16 recurrent tumors. Total RNA was extracted from cryopreserved tissue of adult-type granulosa cell tumor samples. Libraries were prepared from cDNA using the NuGEN Ovation Ultralow Library System V2 (San Carlos, CA). Paired-end bulk RNA sequencing was performed on the Illumina HiSeq 2000 platform. RNA sequencing reads were aligned to the hg19/GRCh37 reference human genome using the STAR software (version 2.6.0b) with default parameters. Samples description: GCT001 Adult-type Granulosa Cell Tumor: recurrent tumor GCT002 Adult-type Granulosa Cell Tumor: primary tumor GCT003 Adult-type Granulosa Cell Tumor: recurrent tumor GCT004 Adult-type Granulosa Cell Tumor: primary tumor GCT005 Adult-type Granulosa Cell Tumor: recurrent tumor GCT006 Adult-type Granulosa Cell Tumor: recurrent tumor GCT007 Adult-type Granulosa Cell Tumor: primary tumor GCT008 Adult-type Granulosa Cell Tumor: recurrent tumor GCT009 Adult-type Granulosa Cell Tumor: recurrent tumor GCT010 Adult-type Granulosa Cell Tumor: recurrent tumor GCT011 Adult-type Granulosa Cell Tumor: primary tumor GCT012 Adult-type Granulosa Cell Tumor: recurrent tumor GCT013 Adult-type Granulosa Cell Tumor: recurrent tumor GCT014 Adult-type Granulosa Cell Tumor: recurrent tumor GCT015 Adult-type Granulosa Cell Tumor: recurrent tumor GCT016 Adult-type Granulosa Cell Tumor: recurrent tumor GCT017 Adult-type Granulosa Cell Tumor: recurrent tumor GCT018 Adult-type Granulosa Cell Tumor: primary tumor GCT019 Adult-type Granulosa Cell Tumor: recurrent tumor GCT020 Adult-type Granulosa Cell Tumor: primary tumor GCT021 Adult-type Granulosa Cell Tumor: primary tumor GCT022 Adult-type Granulosa Cell Tumor: recurrent tumor GCT023 Adult-type Granulosa Cell Tumor: recurrent tumor GCT024 Adult-type Granulosa Cell Tumor: primary tumor

  Dataset EGAD00001009108

• RUNX1 mutated families show phenotype heterogeneity and a somatic mutation profile unique to germline predisposed AML

  We present the clinical phenotypes and genetic mutations detected in 10 novel RUNX1 mutated FPD-MM families. Genomic analyses on these families detected two partial gene deletions, three novel mutations and five recurrent mutations as the germline RUNX1 alterations leading to FPD-MM. On 15 individuals, across the 10 families, we performed additional whole exome or myeloid panel sequencing on blood or bone marrow to determine somatic mutations that co-exist with the germline RUNX1 mutation in tumour and pre-leukaemic states.

  Study EGAS00001004273

• WES data

  WES FASTq files of 76 bulk pre-treatment tumors and 76 matched peripheral blood mononuclear cells from GO30140 group A

  Dataset EGAD00001008129

• Ribosomal profiling on Epstein-Barr virus transformed B-lymphoblastoid cell lines.

  This dataset contains Ribo-seq BAM files of Epstein-Barr virus-transformed B-lymphoblastoid cell lines from six individuals (HG00114, HG00282, NA12005, NA12044, NA12717 and NA12751) of the GEUVADIS Project. For each EBV-LCL, 20 million cells were treated with 2 μg/ml harringtonine and 100 μg/ml cycloheximide. After lysing cells in lysis buffer supplemented with 100 μg/ml cycloheximide, ribosome complexes were purified by density purification. Small RNA molecules were isolated using the NucleoSpin miRNA Kit (Bioke, Leiden, Netherlands), followed by RNA PAGE gel separation. Universal linkers were added after dephosphorylation. After reverse transcription, the cDNA was circularized and, after ribosomal RNA depletion, barcoded and sequenced on Illumina NextSeq 500.

  Dataset EGAD50000000465

• Canadian prostate cancer samples (CPC-GENE) for PanProstate study

  CPC-GENE has sequenced 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 also has sequenced 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 EGAS00001003037

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  arious peripheral blood immune cell subsets from 5 rheumatoid (RA) donors were collected ("CD16p_Mono", "CL_Mono???, "DN_B", "Fr_II_eTreg???, "mDC???, "Mem_CD4" , "Naive_B" , "Naive_CD4" , ???Neu", "NK" , "pDC" , "Plasmablast", ???SM_B", "Tfh", "Th1", "Th17", "Th2" , "USM_B"). The patients were analyzed again longitudinally after abatacept treatment. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.

  Study JGAS000602

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  Various peripheral blood immune cell subsets from 39 healthy volunteers and 50 rheumatoid (RA) donors were collected ("CD16p_Mono", "CL_Mono???, "DN_B", "Fr_II_eTreg???, "mDC???, "Mem_CD4" , "Naive_B" , "Naive_CD4" , ???Neu", "NK" , "pDC" , "Plasmablast", ???SM_B", "Tfh", "Th1", "Th17", "Th2" , "USM_B"). 15 RA patients were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.

  Study JGAS000598

• ANGIOPREDICT - an FP7-funded project enabling personalised medicine for patients with metastatic colorectal cancer.

  In ANGIOPREDICT, academic cancer biologists and industry-based biotechnology researchers will work together with clinicians to identify biomarkers to predict whether individual metastatic colorectal cancer patients will respond positively to Avastin® combination therapy. Diagnostic tests using these biomarkers will also be developed to provide clinicians with the means to predict patient treatment responses in the future.

  Study EGAS00001005423

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

  We performed single cell RNA sequencing (scRNA-seq) from bone marrow on 11 pediatric (0-14 years-old) and adolescent and young adult (AYA) (15-39 years-old) de novo AML samples (Dx) (4 inv(16), 3 t(8;21) and 4 rMLL). In addition, for some patients also relapse sample was sequenced (2 inv(16), 2 t(8;21) and 3 rMLL). Cells were sorted into CD34+/CD38- and CD34-/CD38+ and sequenced separately.

  Dataset EGAD00001008514

• Use of Deep Sequencing to Dectect Clonal Mutations In Sun Exposed Skin Epidermis PART2

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Dataset EGAD00001000825

• Dataset for upper_gastrointestinal_tumor-RNA

  Rare cancer sequencing data of 44 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008853

• Dataset for Sarcoma-WES linked from study EGAS00001004813

  Sequencing data of 144 sarcoma tumor and control runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

  Dataset EGAD00001010258

• Use of Deep Sequencing to Dectect Clonal Mutations In Sun Exposed Skin Epidermis

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Dataset EGAD00001001090

• Laser Capture Microscopy (LCM)-RNAseq for Topological Mapping of Synovial Pathology during Rheumatoid Arthritis

  Synovial tissue from the hip or knee was collected from rheumatoid arthritis (RA) and osteoarthritis (OA) patients at the time of joint replacement surgery. Samples were analyzed using laser capture microdissection (LCM) followed by RNA-seq to evaluate the transcriptome in distinct synovial compartments. Results indicated that synovial compartments have both shared and distinct transcriptional signatures that correspond to key pathways relevant to RA pathogenesis.

  Study phs003587

• WES analysis of tumor samples from ER+ breast cancer patients treated with CDK4/6 inhibitor

  We performed whole exome sequencing of paired fresh frozen tumor from 4 ER+ advanced breast cancer patients. Samples were obtained for each patient prior to combined CDK4/6 inhibitor and endocrine therapy and at disease progression (N=8). DNA was extracted using the Maxwell® RSC FFPE and Tissue DNA Kit (Promega). WES was performed at the Department of Molecular Medicine, Aarhus University Hospital on matched tumor DNA (derived from primary fresh frozen and FFPE tissue) and buffy coat DNA. Libraries of tumors and matching germline DNA were prepared using 50 ng DNA and captured by Twist Comprehensive Exome with custom spike-ins, sequenced on the Illumina NovaSeq 6000 platform to an average coverage of 413x (range: 148-515x). The dataset include the analysis data files (vcf files).

  Dataset EGAD50000000622

• Five Mantle Cell Lymphoma Patients Before and After Failure of Standard Chemotherapy

  MCL cells were isolated from different tissues of five patients with MCL at diagnosis, and at the time of the first clinical relapse after failure of standard immunochemotherapy based on alternation of R(ituximab)-CHOP and R-high-dose-araC. All patients signed informed consent according to the Declaration of Helsinki. Four patients were diagnosed with classical nodal aggressive MCL, and all these patients experienced early relapse (i.e., progression of disease POD < 12 months). One patient was diagnosed with indolent non-nodal MCL and relapsed 9 years after initial MCL diagnosis. The dataset presents single cell RNA sequencing data as well as whole exome sequencing data for these five patients.

  Dataset EGAD50000001213

• Dataset for soft_tissue_tumor-WHOLE_GENOME

  Rare cancer sequencing data of 142 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008900

• Pooled Single-Cell RNA-Seq of iPSC-Derived Neural Stem Cells from ADHD and Control Individuals

  This dataset contains FASTQ files from pooled single-cell RNA sequencing (scRNA-seq) of neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSCs). The iPSCs were reprogrammed using the non-integrative Sendai virus system (CytoTune-iPS 2.0), introducing OCT3/4, SOX2, KLF4, and cMYC. Donor somatic cells included keratinocytes, PBMCs, and lymphoblastoid cell lines from individuals with ADHD and age-matched healthy controls (6–18 years). iPSCs underwent standard quality control, including immunocytochemistry, qRT-PCR, mycoplasma testing, and SNP genotyping. NSCs were produced via neural induction and validated by qRT-PCR and immunostaining for PAX6, SOX2, NESTIN, TUJ1, and FOXG1. Sequencing was performed on the Illumina NovaSeq 6000.

  Dataset EGAD00001015644

• Dataset for melanoma-RNA

  Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008858

• Sequence data from stage I of the CCTG BR.36 ctDNA-directed, multi-center phase II study of molecular response adaptive immunotherapy in non-small cell lung cancer

  The dataset for the study "Early ctDNA molecular response captures therapeutic response in the first stage of CCTG BR.36 ctDNA-directed, multi-center phase II study of molecular response adaptive immunotherapy in non-small cell lung cancer", includes 134 bam files from hybrid capture targeted error-correction next-generation sequencing (PGDx Elio plasma resolve) from plasma cell-free DNA and matched white blood cell DNA from 35 individuals with non-small cell lung cancer on the BR.36 trial, alongside 11 bam files from targeted next generation sequencing (PGDx Elio tissue complete) of tumor DNA from 11 individuals with non-small cell lung cancer on the BR.36 trial.

  Dataset EGAD00001011359

• Dataset for gynecologic_cancer-RNA

  Rare cancer sequencing data of 48 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008856

• Dataset for hematopoietic_malignancy-RNA

  Rare cancer sequencing data of 47 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008860

• 5 scRNA-seq with TCR Enrichment of Tumour-Involved Lymph Nodes, Malignant Seromas and Patient-Derived Xenografts from 18 T-Cell Lymphoma Patients

  This raw data contains 5' scRNA-seq with TCR enrichment data from 18 individual patients analysing cells taken from tumour-involved lymph nodes (LN), malignant seromas and patient-derived xenografts (PDX) including systemic/nodal ALK+ ALCL (n=3 PDX), BIA-ALCL (n=2 seromas), PTCL-NOS (n=5 nodal tumours), nodal T follicular helper lymphoma - angioimmunoblastic type (nTFHL-AI) (n=1), nTFHL, not otherwise specified (nTFHL, NOS, n=1), TLBL (n=5) and 1 case of Sezary Syndrome (SS, cutaneous tumour). Droplet-based 5’ scRNA-seq with TCR enrichment (10x Chromium platform) was performed for all live cells, or the viable CD45+CD3- and CD45+CD3+ fractions following cell sorting by flow cytometry.

  Dataset EGAD00001015703

• sWGS of OV04 patient samples for ACN rascal study

  This dataset contains 142 .bam files of shallow WGS data (~0.1X) from OV04 patient samples. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008121

• Linked-Read Whole Genome Sequencing Profiles Structural Variant Landscape of Gliomas with Barcode-Level Evidence

  Structural variants (SVs) play essential roles in glioma oncogenesis and offer prognostic insights, yet the SV landscape of gliomas has not been completely characterized due to previous technological limitations. To comprehensively profile the SV landscape of gliomas, we performed linked-read whole genome sequencing (LR-WGS) on 31 tumour samples from 20 glioma patients. Using barcode-level evidence, we validated known SVs and identified the presence of extrachromosomal DNA containing the EGFR sequence, which correlates with elevated EGFR expression. Additionally, we uncovered rare SVs affecting genes typically mutated by single nucleotide variants (SNVs), including those in the SWI/SNF chromatin remodeling complex. Our analysis also reveals selective chromosomal vulnerabilities to SVs, highlighting certain chromosomes as hotspots for SV accumulation. Collectively, our results demonstrate the utility of LR-WGS in accurately detecting SVs and thoroughly profiling SV landscapes using barcode-level evidence. The insights gained into the synergistic effects of SNVs and SVs on oncogenes further underscore the importance of integrating SV analysis when examining mutations in gliomas.

  Study EGAS50000000947

• Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

  Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n=17) and DNA methylation (whole-genome bisulphite sequencing, n=10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.

  Study EGAS00001002592

• atrial appendage RNA-seq in non-, paroxysmal and persistent atrial fibrillation

  Understanding the interconnectedness of structural remodelling processes atrial fibrillation (AF) in patients could identify targets for future therapies. These data include transcriptome sequencing of atrial tissues of patients without AF, with paroxysmal AF and persistent AF (total n=64). In AF patients, epicardial cell gene expression decreased, contrasting with an upregulation of epithelial to mesenchymal transition (EMT) and mesenchymal cell gene expression. Immunohistochemistry demonstrated thickening of the epicardium and an increased proportion of (myo)fibroblast-like cells in the myocardium, supporting enhanced EMT in AF. We furthermore report an upregulation of endothelial cell proliferation, angiogenesis and endothelial signalling. EMT and endothelial cell proliferation concurred with increased interstitial (myo)fibroblast-like cells and extracellular matrix gene expression including enhanced tenascin-c, thrombospondins, biglycan and versican. Morphological analysis discovered increased and redistributed glycosaminoglycans and collagens in the atria of AF patients. Signalling pathways, including cell-matrix interactions, PI3K-AKT and Notch signalling, that could regulate mesenchymal cell activation, were upregulated. These dynamic processes may provide targets to prevent or reverse structural remodelling.

  Study EGAS00001005295

• Competitive selection of somatic mutant clones in normal human skin varies with body site

  The risk of getting non-melanoma skin cancer varies over 40-fold across the body. Here we map mutations in normal skin in high and low risk sites in normal donors and those with an increased risk of skin cancer. The density of mutations varied widely, with evidence of positive and negative genetic selection.  Regional differences in mutational signatures in high and low cancer risk sites and preferential selection of mutants of TP53 in high risk skin and FAT1 in lower risk skin were observed. 10% of clones had copy number changes in cancer associated genes and the largest had multiple driver mutations with loss of heterozygosity. In hair follicles, a proposed site of origin of skin cancers, mutations in the upper follicle resembled adjacent skin, but the lower follicle was sparsely mutated. We conclude cancer risk reflects the efficiency of transformation of oncogenic mutants rather than the density of mutant clones.

  Dataset EGAD00001006194

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

  RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (Kapa Biosystems, Wilmington, MA) and sequenced to a target depth of 200-M reads on the Illumina HiSeq platform (Illumina, San Diego, CA).

  Dataset EGAD00001008512

• DNA methylation changes upon growth hormone treatment in children with idiopathic short stature

  This dataset includes DNA methylation profiles before and after GH treatment (with a duration of ~18 months in average) on 47 healthy children using customized methylC-seq capture sequencing. It includes 360 fastq files (i.e. 180 paired-end fastq files) where 40 fastq files were generated with HiSeq and 320 fastq files were generated with NovaSeq.

  Dataset EGAD00001008641

• Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis

  Whole-genome sequence (WGS) analysis of tumors from 22 TP53 mutation carriers. We observed somatic mutations affecting Wnt, PI3K/AKT signaling, epigenetic modifiers and homologous recombination genes as well as mutational signatures associated with prior chemotherapy. We identified near-ubiquitous early loss of heterozygosity of TP53, with gain of the mutant allele. This occurred earlier in these tumors compared to tumors with somatic TP53 mutations, suggesting the timing of this mark may distinguish germline from somatic TP53 mutations. Phylogenetic trees of tumor evolution, reconstructed from bulk and multi-region WGS, revealed that LFS tumors exhibit comparatively limited heterogeneity. Overall, our study delineates early copy number gains of mutant TP53 as a characteristic mutational process in LFS tumorigenesis, likely arising very early in life or in utero.years prior to tumor diagnosis.

  Dataset EGAD00001009280

• Single-Nuclei RNA Sequencing and Spatial Transcriptomics of Human Heart Right Atrial Appendage and Pericardial Fluid in Cardiovascular Disease

  This dataset includes single-nuclei RNA sequencing (snRNA-seq) and spatial transcriptomics data from biopsies of the right atrial appendage and pericardial fluid, collected during open-heart surgeries. The samples represent various clinical contexts, including control, ischemic heart disease, heart failure, and myocardial infarction. For each biopsy, nuclei were isolated, and RNA sequencing libraries were prepared using the 10x Genomics Chromium v3 platform. Additionally, spatial transcriptomics was performed on the heart samples. The dataset provides raw sequencing data, which includes fastq files generated from these libraries, offering valuable insights into the cellular composition of heart tissues and associated fluids across different disease states.

  Dataset EGAD50000000927

• Spatial omics analysis of non-small cell lung cancers for revealing molecular statuses of intratumor heterogeneity and tumor microenvironment

  In this study, we perform spatial transcriptome analysis Visium/Xenium and other omics analysis using surgical specimens of Japanese non-small cell lung cancer cases to understand omics statuses of cancer cells and their surrounding stromal and immune cells in local tumor regions. We aim to stratify lung cancer patients with considering intratumor heterogeneity and complicated microenvironent of lung cancer tissues by using spatial omics data and histopathological information.

  Study JGAS000613

• Molecular analyses of stage IIIa NSCLC patients treated with neoadjuvant chemmoimmuntherapy

  This dataset comprises molecular and immunogenomic profiles from 60 individual NSCLC patients (30 male, 30 female), with samples collected at multiple timepoints including initial biopsies (IB), resections (RES), and peripheral blood mononuclear cells (PBMC) at different timepoints during treatment. It includes 32 FFPE tumor samples sequenced on Illumina with the FoundationOne panel, 20 FFPE samples sequenced on IonTorrent with the Oncomine Comphrehensive Assay Plus, and 41 samples assessed with IonTorrent via Oncomine Immune Response Research Assay panel for targeted gene expression. T-cell receptor (TCR) repertoire profiling was performed on 62 tumor samples (initial biopsies and resections, Oncomine TCR Beta-SR Assay), and 155 blood-derived samples were sequenced with Oncomine TCR Beta-LR Assay. Data files include processed sequencing results in bam format.

  Dataset EGAD50000001630

• 4 - transcriptome (.bam) files, 2 -called somatic mutations (.vcf) files and 2 coverage (.csv) files

  The dataset contains 4 .bam whole transcriptome files that were generated from 2 tumor samples (one .bam file per sample was created using exome-capture (hybrid capture) and the other .bam file was created using ribo-repletion (inverse mRNA selection) library preparation technology). The dataset also contains 2 somatic mutations (.vcf - sample) files (one per sample) which serve as input for Vardetector package (vardetector/vardetector at main · julijselb/vardetector) to produce somatic coverage over those mutations from the .bam file. Therefore, the dataset also contains 4- .csv files (number of reads per somatic mutation that contain the somatic mutation variant and the ones that do not contain the somatic mutation variant) that serve as outputs of the Vardetector package.

  Dataset EGAD50000002055

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the feature of age-associated helper T (ThA) cells and its contribution to autoimmune diseases, CD4+ T cell subsets from 19 rheumatoid arthritis (RA), 62 systemic lupus erythematosus (SLE), 40 idiopathic inflammatory myopathy (IIM) and 64 healthy controls (HC) were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA). RNA-seq was performed with each CD4+ T cell subset samples.

  Study JGAS000626

• Research for drug discovery and elucidation of pathophysiology using disease-specific iPS cells

  We investigated roles of KRAS on stemness maintenance and differentiation propensity in the context of induced pluripotent stem cells (iPSCs) using isogenic KRAS mutant (G13C/WT) and wild-type (WT/WT) iPSCs from the same RAS-associated autoimmune lymphoproliferative syndrome-like disease (RALD) patients. Exome-seq analysis was conducted to compare gene profiles of WT/WT and G13C/WT iPS cells. We have not found any differences of gene mutation in the two genotypes.

  Study JGAS000136

• Comparative genomics research for Chinese colorectal cancer

  In order to clarify the mechanisms of genesis and development of colorectal carcinoma, in this study, we performed comparative genomics research in Chinese colorectal cancer at various clinical stage via whole exon sequencing or whole genome sequencing. Comparative bioinformatical analysis was perform to find the difference on somatic single-nucleotide variants, short insert/deletion variants, genomic structural variants, and copy number variants between cancer tissue and normal tissue, or among cancer tissues at various clinical stages.

  Study EGAS00001002576

• Comparative genomics research for Chinese colorectal cancer

  In order to clarify the mechanisms of genesis and development of colorectal carcinoma, in this study, we performed comparative genomics research in Chinese colorectal cancer at various clinical stage via whole exon sequencing or whole genome sequencing. Comparative bioinformatical analysis was perform to find the difference on somatic single-nucleotide variants, short insert/deletion variants, genomic structural variants, and copy number variants between cancer tissue and normal tissue, or among cancer tissues at various clinical stages.

  Study EGAS00001002607

• Anthropological dataset 2 for The admixture histories of Cabo Verde

  Datasets used in the article "The genetic and linguistic admixture histories of the islands of Cabo Verde" by Laurent R et al. eLife 2023 (DOI: https://doi.org/10.7554/eLife.79827 - URL: https://elifesciences.org/articles/79827) File name "eGAdeposit_233CaboVerde_GEOcoordFULL_FINAL_01062022.txt" Column 1 corresponds to individual alphanumeric codes as in the "eGAdeposit_233CaboVerde_GenotypeFile_FINAL_01062022.vcf" genotype file Column 2-3 corresponds to X-Y GPS coordinates of individual's interview location in Cabo Verde Column 4-5 corresponds to X-Y GPS coordinates of individual's self-reported residence location at the time of the interview Column 6-7 corresponds to X-Y GPS coordinates of individual's self-reported birth-place location Column 8-9 corresponds to X-Y GPS coordinates of individual's self-reported paternal birth-place location Column 10-11 corresponds to X-Y GPS coordinates of individual's self-reported maternal birth-place location

  Dataset EGAD00001008977

• Dataset for bone_cancer-RNA

  Rare cancer sequencing data of 55 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008848