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• 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

• 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

• RNA-sequencing on thyroid samples from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality

  The current data pertains RNA-sequencing reads obtained from thyroid samples acquired from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality. Total RNA was isolated from left lobe from thyroid samples using a hand-held homogenizer and the Promega ReliaPrep RNA Miniprep System (Thermo Fisher Scientific). RNA yield was determined with the NanoDrop Microvolume Spectrophotometer (Thermo Fisher Scientific). Fragmentation and mRNA library preparation was performed using the Kapa mRNA Hyperprep Kit (Roche, Basel, Switzerland). Libraries were equimolar pooled and quality was checked on a TapeStation system using the DNA1000 ScreenTape (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with poly(A) selection to sequence all messenger RNA for gene expression analysis on the NovaSeq6000 PE150 (Illumina, San Diego, CA, USA), producing at least 40M 150-bp paired-end reads per library.

  Dataset EGAD50000000387

• SNV and indel calls from 8086 individuals in the British Autozygosity Populations BioResource dataset

  This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies: 1. 3781 British Pakistani/British Bangladeshi adults from East London Genes and Health 2. 2791 British South Asian mothers from Born in Bradford 3. 1428 British South Asian adults from Birmingham 4. 86 individuals (mixed ancestries) from families with rare diseases, from Queen Mary University London All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866. Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true: SNPs: "QD < 2.0 || FS > 30 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" Indels: "QD < 2.0 || FS > 30 || ReadPosRankSum < -20.0"

  Dataset EGAD00001004581

• The Natural History of Human Prostate Cancer

  Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of 3 men. For each of three different prostates, multiple tumour samples (4, 5, and 3 depending on the case) and one normal tissue sample were whole genome sequenced with a matched blood sample using the Illumiuna HiSeq platform. Tumour samples were sequenced to a target depth of 50X and normals and blood to a target depth of 30X. As of September 2020, some of the studies using these data include: Cooper et al, Nature Genetics 2015 (PMID: 25730763) Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)

  Dataset EGAD00001000689

• Early Detection of Malignant and Pre-Malignant Peripheral Nerve Tumors Using Cell-Free DNA Fragmentomics

  Early detection of neurofibromatosis type 1 (NF1) associated peripheral nerve sheath tumors (PNST) informs clinical decision-making, potentially averting deadly outcomes. Here, we describe a cell-free DNA (cfDNA) fragmentomic approach which distinguishes non-malignant, pre-malignant and malignant forms of NF1 PNST. Using plasma samples from a novel cohort of 101 NF1 patients and 21 healthy controls, we validated that our previous cfDNA copy number alteration (CNA)-based approach identifies malignant peripheral nerve sheath tumor (MPNST) but cannot distinguish among benign and premalignant states. We therefore investigated the ability of fragment-based cfDNA features to differentiate NF1-associated tumors including binned genome-wide fragment length ratios, end motif analysis, and non-negative matrix factorization deconvolution of fragment lengths. Fragmentomic methods were able to differentiate pre-malignant states including atypical neurofibromas (AN). Fragmentomics also adjudicated AN cases suspicious for MPNST, correctly diagnosing samples noninvasively, which could have informed clinical management. Overall, this study pioneers the early detection of malignant and premalignant peripheral nerve sheath tumors in NF1 patients using plasma cfDNA fragmentomics. In addition to screening applications, this novel approach distinguishes atypical neurofibromas from benign plexiform neurofibromas and malignant peripheral nerve sheath tumors, enabling more precise clinical diagnosis and management.

  Study phs003712

• Space Associated Stem Cell Hallmarks of Aging in Astronauts

  This study examined the effects of the stress of space, specifically low earth orbit, on hematopoietic stem and progenitor cells (HSPCs) that maintain lifelong hematopoiesis and immune responses. Enriched CD34+ HSPCs were derived from 7 astronauts before, during and after 10 and 21-day ISS missions on the International Space Station. The samples were used as input to whole transcriptome sequencing by bulk RNA-Seq performed at The Scripps Research Institute Next Generation Sequencing Core on Illumina NextSeq 2000 sequencer and single cell RNA-Seq performed at The Salk Institute for Biological Studies on Illumina NovaSeq X Plus sequencer. Subsequent expression, RNA editing, and retrotransposon analyses were performed to assess HSPC and immune subpopulation survival dynamics. Overall, these analyses revealed space-associated stem cell hallmarks of aging (SASHA), including spaceflight dependent alterations in HSPC survival and self-renewal, ADAR1, telomere maintenance, mobilization and cell cycle gene expression, combined with space-induced clonal hematopoietic mutations, APOBEC3C activation and retrotransposon deregulation to warrant countermeasure development to enable long-duration spaceflight. Post-spaceflight analysis revealed increased C-to-T and clonal hematopoiesis-associated mutations, repetitive element and base deaminase deregulation, decreased telomere maintenance gene expression, and decreased self-renewal capacity compared to ground controls. These results demonstrate the space-associated aging effects in HSPCs after month-long exposure to LEO, providing insights into utilizing the LEO environment to model space-accelerated aging and other age-related malignancies.

  Study phs004267

• MGHBoston_Molpheno_Closed

  This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data of 17 lymphoblastoid cell lines derived from patients with complex genomic rearrangements. Patients have phenotypes in category of intellectual disability and/or multiple congenital anomalies. Data access is closed.

  Dataset EGAD00001004866

• Identification and functional characterisation of a rare MTTP variant underlying familial non-alcoholic fatty liver disease

  We identified a rare causal variant in MTTP, c.1691T>C p.I564T (rs745447480) encoding microsomal triglyceride transfer protein (MTP) causing progressive non-alcoholic fatty liver disease with cirrhosis and hepatocellular carcinoma unrelated to metabolic syndrome, without manifestations of abetalipoproteinemia, in a four generation family with South Asian ancestry. Variant-expressing hepatocyte-like-cells (HLCs) derived from human induced pluripotent stem cells generated from homozygous donor skin fibroblasts had lower lipoprotein ApoB secretion, compared to wild type cells. Cytoplasmic triglyceride accumulation in HLCs triggered endoplasmic reticulum stress, secretion of pro-inflammatory mediators, production of reactive oxygen species, delineating the progression of disease associated with homozygosity for MTTP p.I564T

  Study EGAS00001005254

• A whole-genome sequencing study for evolutionary history of Tibetans and their genetic adaptations to high altitude

  Due to a unique adaptation to high altitude, the Tibetan Plateau population has been the subject of much research interest. In this study, we conducted whole genome sequencing of 27 Tibetan individuals. Through our analysis, we inferred a detailed history of demography and revealed the natural selection of Tibetan population. We provided evidence of genetic separation between the two subpopulations of Han and Tibetans as early as 44 to 58 thousand years ago, replicated previously reported high altitude adaptation genes, including EPAS1 and EGLN1, and reported three new candidate genes, including PTGIS, VDR, and KCTD12.

  Study phs001338

• 909 bulk mRNA sequencing samples from the UPTIDER program

  Raw sequencing data for 909 bulk mRNA samples that correspond to 749 metastases, 64 primary tumours and 96 normal tissue. These samples were sequenced using NovaSeq6000. Library was prepared with Lexogen QuantSeq 3' FWD. Raw single-end fastq samples have been deposited as gzipped files.

  Dataset EGAD50000001910

• Sample metadata

  Sample metadata for this experiment. Includes treatment and donor derivation information.

  Dataset EGAD50000000827

• CHIC_TPO3_2023

  Human engineered CRC organoids (APC KO; KRAS G12D; TP53 KO) were grown in glucose, lactate or with DCA. Samples were collected 7 hours after the treatments and processed for bulk CHIC-seq.

  Dataset EGAD50000000090

• Sequencing data for oesophageal and related samples - BOs release 2 (RNA)

  Dataset EGAD00001003840

• EGAD00000000047

  Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples

  Dataset EGAD00000000047

• Dataset of whole genome bisulfite data of 4 different monocyte samples

  Regions of common inter-individual DNA methylation differences in human monocytes – potential function and genetic basis WGBS Data of Samples: 43_Hm03_BlMo_Ct, 43_Hm02_BlMo_Ct, 43_Hm05_BlMo_Ct, 43_Hm01_BlMo_Ct For details about sequencing or sample metadata check http://deep.dkfz.de/

  Dataset EGAD00001003259

• NIHR-BioResource Rare Diseases - Neurodevelopmental disorders

  This dataset contains short-read whole-genome sequencing data for individuals with neurodevelopmental disorders and their relatives from the NIHR-BioResource Rare Disease Consortium.

  Dataset EGAD00001004456

• Reference DNA standards for GCLP pipeline

  The use of reference DNA standards generated from cancer cell lines sequenced in the Cancer Genome Project to establish the sensitivity, specificity, accuracy and reproducibility of the WTSI GCLP sequencing pipeline

  Dataset EGAD00001002015

• Chromatin 3D interactions mediate genetic effects on gene expression (RNA-seq)

  RNA-seq data for 168 Lymphoblastoid Cell Lines (LCL) and 78 Fibroblasts (FIB) from the Gencord Cohort. This dataset was generated as part of the following study: Delaneau et al (2019). Chromatin 3D interactions mediate genetic effects on gene expression.

  Dataset EGAD00001004872

• The South Asia Rheumatic Heart Disease Genetics Network Data

  This dataset comprises over 850 individuals recruited in Uttar Pradesh, India, including cases of rheumatic heart disease based on echocardiographic diagnosis and controls recruited on the basis of normal echocardiograms. For this analysis all available samples were genotyped using the Illumina HumanCore-24 BeadChip platform.

  Dataset EGAD00001004882

• Predictor_RIO_TNBC (2019-04-03)

  In this study, samples fom a window study of the PARP inhibitor rucaparib in patients with primary triple negative or BRCA1/2 related breast cancer (RIO trial) will be investigated. Samples will undergo whole genome sequence and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004894

• Wilms Tumour organoid sequencing WGS (2019-09-05)

  This study investigates the genomic and transcriptomic characteristics of Wilm's tumour organoids . This dataset contains all the data available for this study on 2019-09-05.

  Dataset EGAD00001005312

• Panel sequencing data for Molecular Characterization of ETMRs

  This dataset contains panel sequencing data from 33 samples. Targeted sequencing was performed by creating libraries using the Agilent SureSelect XT technology. Libraries were sequenced using molecular barcode-indexed ligation-based sequencing using a NextSeq500 (Illumina) instrument. Between three and six lanes per sample have been sequenced resulting in 262 Fastq files (paired end).

  Dataset EGAD00001006208

• HV31 - 10x linked-read sequencing

  10x linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~40×. Sequencing was performed at Bart’s and the London Genome Centre on the Illumina HiSeq platform.

  Dataset EGAD00001007046

• ChIP-sequencing in human monocyte differentiation

  This dataset consists of ChIP-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. ChIP-sequencing was done for H3K27, RAD21 and CTCF. In total, the data set includes 120 samples.

  Dataset EGAD00001007954

• Raw count matrix for 44 baseline + 44 progression samples

  Count matrix from 44 pre-treatment (Ven-Obi or Clb-Obi) and 44 paired, post-treatment relapsed CD19+ B cells.

  Dataset EGAD00001009500

• RNA-seq data for 67 patient cohort

  This dataset includes RNA-seq data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)

  Dataset EGAD00001008648

• WGS data for 67 patient cohort

  This dataset includes WGS data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)

  Dataset EGAD00001008647

• CTCF ChIP-sequencing data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains CTCF ChIP-sequencing data from seven samples (six tumor samples and one tumor derived cell line). Following library amplification, DNA fragments were sequenced using Illumina HiSeq 2000 paired-end sequencing resulting in 14 FASTQ files.

  Dataset EGAD00001008806

• Exome sequencing data

  Libraries were constructed using SureSelect HS XT Target Enrichment System v6 (Agilent). For each patient a library of CD3- cells (myeloid cells, considered tumor cells) and CD3+ cells (T cells, considered healthy) were generated.

  Dataset EGAD00001010190

• Whole exome sequencing (WES) of CIMP leukemias

  Whole exome sequencing of tumor material derived from 14 mixed myeloid/lymphoid leukemias with a CpG Island Methylator Phenotype (CIMP). For 4 of these patients, normal material was also sequenced and used as control (files with the same identifiers prepended by an “h”).

  Dataset EGAD00001011053

• WES for CNV-verified CTCs enriched by high-throughout microfluidic device from entire cancer patient leukopak

  WES analysis (illumina platform, PE150, 100x coverage) was performed on a pool of copy number variation (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).

  Study EGAS50000000724

• Single-cell RNA sequencing of metastatic colorectal cancer organoids treated with cetuximab

  Organoids were seeded in 12-well plates at a density of 5 × 10⁴ cells per well, embedded in 200 µL of Matrigel diluted 1:1 with culture medium, and maintained under EGF-deprived conditions. After four days of growth, organoids were either left untreated or treated with cetuximab (20 µg/mL). Following 72 hours of treatment, organoids were harvested, dissociated, and live single cells were sorted for single-cell RNA sequencing using the 10x Genomics platform.

  Dataset EGAD50000002104

• RNASeq_EGAS00001001306

  RNASeq sequencing. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2 × 76 bp. We generated more than 20 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina Inc.) following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files.

  Dataset EGAD00001001443

• Pervasive H3K27 acetylation and ERV expression in H3.3K27M gliomas present a therapeutic vulnerability

  We sequenced a total of 2 H3.3K27WT (pcGBM2, G477; 3 replicates total) and 2 H3.3K27M (DIPGVI, DIPGXIII; 6 replicates total) patient-derived cell lines as well as Crispr/Cas9 H3.3K27M-KO clones for one of the cell lines (3 replicates total; DIPGXIII-KO) using ATAC-Seq. P-XX designates passages of replicates. These samples can be found at GEO under accession number GSE128744. This repository contains 1 replicate of G477 to be released under controlled access.

  Dataset EGAD00001004961

• NIHR BioResource Rare Diseases WGS project - Ehler-Danlos (ED) and ED-like Syndromes (EDS) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Ehler-Danlos (ED) and ED-like Syndromes (EDS) Rare Disease domain.

  Dataset EGAD00001005123

• WES data from 165 tumor/germline samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.

  Dataset EGAD00001006239

• Sequencing data for oesophageal and related samples - Katz-Summercorn, Jammula et al (WGS)

  Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. WGS (BAM files)

  Dataset EGAD00001006349

• Resequencing (MIPS) of candidate genes for Keratoconus (2020)

  The dataset consists of the BAM-files of 745 patients and 810 controls (retained after quality control) of a set of 34 candidate genes obtained after targeted enrichment via Molecular Inversion Probes (MIPS) technology. The sequencing was performed on the NextSeq 500 (Illumina, CA, USA) using custom sequencing and index primers in three 2 x 76 bp, dual indexed runs using a 150 cycles High-Output Illumina kit (Illumina, CA, USA). Alignment of the fastq reads to the human genome was performed using BWA (v0.7.4).

  Dataset EGAD00001006825

• mRNA-Seq on single human MII oocytes collected from gonadotropin stimulated women

  This dataset contains 11 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from gonadotropin stimulated women undergoing fertility treatments. M-II stage oocytes were collected and flash frozen prior to lysis followed by 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 EGAD00001006863

• Single cell study of infant leukemias

  We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.

  Dataset EGAD00001007854

• Sequencing data for oesophageal and related samples - OACs 496 release (WGS)

  Data from 496 OCCAMS (Oesophageal Cancer Clinical And Molecular Stratification) cases. WGS BAM files 496x oesophageal adenocarcinoma samples 496x normal samples

  Dataset EGAD00001007785

• Prevalence of transthyretin amyloidosis in patients with heart failure and no left ventricular hypertrophy

  The study prospectively enrolled patients admitted for HF with LV ejection fraction (LVEF) ≥ 50% and LV wall thickness <12 mm. TTR cardiac amyloidosis was diagnosed according to accepted criteria, which include positive cardiac 99-Tc-DPD scintigraphy in the absence of monoclonal protein expansion in blood. In a cohort of patients with HFpEF without LVH, the prevalence of TTR cardiac amyloidosis was 5%. Transthyretin gene sequencing was performed in positive patients.

  Dataset EGAD00001007787

• Organoid Derivation Project: TGS (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 EGAD00001011089

• Organoid Derivation Pilot: RNAseq (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 EGAD00001011091

• Organoid Derivation Project - GRCh38 - TGS (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 EGAD00001011094

• Whole genome sequencing of tumor samples from advanced pre-treated NSCLC patients recruited in a phase I/II single-arm trial utilising CVA21, an oncolytic coxsackie virus, in combination with pembrolizumab.

  This dataset contains paired tumor and matched normal whole-genome sequencing (WGS) data from longitudinally collected samples of patients enrolled in an Australian clinical study involving multiple cancer types. For each patient, one or more tumor biopsies were obtained at different treatment time points (Scr, Day 0, Day 15, Day 22, Day 33), and matched normal samples were collected either from blood or non-tumor tissue.

  Dataset EGAD00001015682

• Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures

  The SARS-CoV-2 pandemic has led to increasing numbers of COVID-19 patients all over the world. Aetiopathologies range from no symptoms, mild flu-like to severe cases succumbing to respiratory failure. Reports on a dysregulated immune system in the severe cases, showing similarities to cytokine release syndrome, calls for better characterization and understanding of the changes in the immune system as well as their variance across COVID-19 patients in order to be able to design according to host-directed therapies. Here, we profiled blood transcriptomes of 39 COVID-19 patients and 10 control donors. Enriched granulocyte signatures in whole blood samples were verified in granulocyte samples from 49 COVID-19 patients in a second cohort.

  Study EGAS00001004503

• Avelumab or M7824 for People with Recurrent Respiratory Papillomatosis

  This submission includes genomic data derived from the study of clinical samples from two different phase II trials. These trials evaluated the clinical efficacy and safety of avelumab or M7824 in the treatment of adults with recurrent respiratory papillomatosis (RRP). Subjects with aggressive RRP were treated with three to six doses of avelumab or M7824. Pre-treatment or post-treatment snap frozen papilloma and normal mucosa samples were subjected to whole exome sequencing and bulk RNA-seq. A total of twenty subjects were enrolled and treated. 

  Study phs002373

• 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

• Luminal progenitor cell line iHBEC(CD117)

  Basal-like breast cancer originates in luminal progenitors, frequently with an altered PI3K pathway, and focally in close association with genetically altered myoepithelial cells at the site of tumor initiation. The exact trajectory behind this bi-lineage phenomenon remains poorly understood. Here we used a breast cancer relevant transduction protocol including hTERT, shp16, shp53, and PIK3CA(H1047R) to immortalize FACS isolated luminal cells, and we identified a candidate multipotent progenitor. We found that the apparent luminal phenotype of these oncogene transduced progenitors was metastable giving rise to basal-like cells dependent on culture conditions. After culturing the cells for more than 60 passages, cells were subjected to scRNA-seq as well as bulk RNA sequencing of two subpopulations (CD271+ and CD271-).

  Dataset EGAD50000000723

• HipSci whole exome sequencing for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed whole exome sequencing using Agilent whole exome pulldown method.

  Study EGAS00001001726

• HipSci expression microarray for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed expression analysis using the Illumina HumanHT -12 Expression BeadChip.

  Study EGAS00001001729

• 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

• The Genetic Basis of Progression in Multiple Sclerosis

  This study examined the genetic determinants of multiple sclerosis (MS) severity in an international cohort of people with MS assembled by the International Multiple Sclerosis Genetics Consortium (IMSGC) and the MultipleMS Consortium. A total of 12,584 people with MS of European ancestry were included in the main genome-wide association study (GWAS). Participants were enriched for older individuals with longer disease duration (mean age 51.7 years and mean disease duration 18.2 years). All individuals were whole-genome genotyped on the Illumina Global Screen Array (GSAMD-24v2-0). Imputation was performed using the Haplotype Reference Consortium reference panel. The primary outcome was the age-related MS severity score. All individuals had at least 1 expanded disability status scale (EDSS) measure. When multiple EDSS scores were available, the last one was selected to calculate the age-related MS severity score.Of those 12,584 people with MS, this data release includes 4,623 participants recruited from non-European sites in the US, Canada and Australia. This release includes individual-level genotype and phenotype files necessary to replicate our GWAS of MS severity, including covariates.

  Study phs002929

• 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

• SNP array files, IDAT files, from 34 members of a Family with a high prevalence of psychosis

  We investigated the genetic causes of major mental disorders (MMDs) including schizophrenia, bipolar disorder I, major depressive disorder, and attention deficit hyperactive disorder, in a large family pedigree from Alpujarras, South of Spain, a region with a high prevalence of psychotic disorders. We applied a systematic genomic approach based on karyotyping (N=4), genotyping by genome-wide SNP array (N=33), whole-exome sequencing (N=4), and whole-genome sequencing (N=12). We performed genome-wide linkage analysis, family-based association analysis, and polygenic risk score estimates. Significant linkage was obtained at chromosome 9 (9q33.1-33.2, LOD score= 4.11), a suggestive region that contains five candidate genes ASTN2, BRINP1, C5, TLR4, and TRIM32, previously associated to MMDs. Comprehensive analysis associated the MMD phenotype with genes of the immune system with dual brain functions. Moreover, the psychotic phenotype was enriched for genes involved in synapsis. These results should be considered once studying the genetics of psychiatric disorders in other families, especially the ones from the same region, since founder effects may be related to the high prevalence.

  Study EGAS00001004592

• Identification of therapeutic target molecules for prostate cancer by using next generation sequencer

  Comprehensive transcriptional characterization of cancer tissues can reveal important molecular signatures associated with the disease progression. Long non-coding RNA (LncRNA) has a diversity of functions such as transcription, epigenetic and gene regulation in cancer cells including prostate cancer cells. Here, we performed directional RNA-sequence (RNA-seq) on clinical samples obtained from prostate cancer (PC) and lethal castration-resistant PC (CRPC) patients to identify novel molecular signatures including protein coding genes and non-coding RNAs induced in CRPC tissues.

  Study JGAS000198

• 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

• Single cell RNA-seq of 24 samples from 13 individual human embryonic meninges of PCW 5.0-13.0 using 10X chromium technology

  A total of 24 samples of meninges from 13 normal human embryos of post-conceptional week (PCW) 5.0-13.0 were dissected and subject to 10Xgenomics chromium single cell RNA sequencing with the purpose of identifying cell types and gene expression programs for normal meninges development. All libraries were sequenced on an Illumina NovaSeq 6000 using S4 to a target sequencing depth of 100,000 reads/cell. Final data after processing with STARSolo 2.7.10a, using human genome GRCh38.p12 and transcript annotations from ENSEMBL release 93 from reference package GRCh38-3.0.0 as available from 10Xgenomics, consists of 24 BAM files.

  Dataset EGAD50000001434

• GSA pilot raw data

  Unfiltered genotype data for a pilot study (Batch 1) of 1,140 DDD Study participants (and 12 "Empty" samples). Samples include 380 mothers, 382 fathers and 378 probands, and form 376 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.

  Dataset EGAD00010002567

• 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

• 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

• ChIP-seq bulk

  This dataset gather ChIP-seq data produced by immunoprecipitating CTCF factor in own laboratory in MM.1S cell line in EtOH and Dex conditions. It also gather ChIP-seq dataset produced by external laboratory (Active Motif) for H3K27ac mark and GR transcription factor in same cell line and conditions ( MM.1S ETOH/Dex)

  Dataset EGAD00001011136

• BarcUVa-Seq (Biology of Colorectal Cancer Risk Enhancers)

  This study was designed to generate a cohort of normal colon mucosal biopsies from the "average risk" population. Its primary aims included the development of an RNA-seq dataset of normal colon mucosal biopsies across three colon regions (ascending, transverse and descending). Further, we aimed to provide plausible prioritization to genetic components of colorectal cancer risk by employing methods such as expression quantitative trait loci analysis. In doing so, we provide a novel reference dataset for the study of colon cancer risk in the healthy colon epithelium. RNA-seq was performed in batches on an Illumina HiSeq 2500 (batch 1-7) or NovaSeq 6000 (batch 8) on a total of 463 samples. Matched genotyping data was generated on the Illumina OncoArray BeadChip. Phasing was carried out using Minimac 3 and imputation was performed using The Haplotype Reference Consortium panel on the Michigan Imputation Server.Genotype and RNA-seq data will be made available in dbGaP.

  Study phs003338

• MGA-NUTM1 fusion in high grade spindle cell sarcoma

  NUT carcinoma (NC) with mesenchymal differentiation have rarely been described in the literature. In this report, we describe the characterization of two cases of high grade spindle cell sarcoma harboring a novel MGA-NUTM1 fusion. Whole genome sequencing identified the presence of complex rearrangements resulting in a MGA-NUTM1 fusion gene in the absence of other significant somatic mutations. The fusion protein was predicted to retain nearly the entire protein sequence of both MGA (exons 1-22) and NUTM1 (exons 3-8). In contrast to typical cases of NC, these cases were successfully treated with aggressive local control measures (surgery and radiation) and both patients remain alive without disease. These cases describe a new subtype of NUTM1-rearranged tumors warranting expansion of diagnostic testing to evaluate for the presence of MGA-NUTM1 or alternative NUTM1 gene fusions in the diagnostic workup of high grade spindle cell sarcomas or small round blue cell tumors of ambiguous lineage.

  Study EGAS00001003341

• 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

• Mutational analysis of an oligoprogressive sarcomatoid hepatocellular carcinoma treated with an immune checkpoint inhibitor.

  The dataset is composed of three sequenced tumor samples: (I) Meta-bone-557 (bone metastasis obtained from occipital lesion resection during treatment with Liposomal doxorubicin); (II) Meta-CNS-888 (brain metastasis obtained from surgical resection during treatment with Nivolumab); (III) Primary-liver-463 (primary hepatic tumor obtained from surgical resection during treatment with Nivolumab). Genomic DNA from tumor samples was extracted using GeneRead DNA FFPE kit (Qiagen), containing Uracyl-D Glycosylase, according to the manufacturer’s instructions. Whole-exome libraries were prepared using SureSelect XT Clinical Research Exome Target Enrichment kit (Agilent Technologies # 5190-7338). Sequences (150bp paired-end) were generated on a NextSeq 500 sequencing platform (Illumina).

  Dataset EGAD00001006982

• Renal_habitat_WXS

  This project aims at correlating genetic diversity (as well as transcriptomic, metabolic and immune diversity) observed in multiple targeted tumour biopsies and circulating tumour DNA with heterogeneity on multiparametric MRI. To this end, 20 patients with RCC (15 patients with localised/locally advanced disease and 5 with mRCC) will undergo multiparametric MRI including metabolic assessment by 13C-MRSI as well as measurements of tumour perfusion, oxygenation and water diffusion. Based on unique combinations of these imaging parameters, tumour habitats will be defined through cluster mapping. Intra-operative biopsy and immediate freezing of tumour cores from different imaging habitats will be performed. Multiregional ex-vivo tumour biopsies will be spatially registered to the MR data by using 3D printed tumour moulds generated from high-resolution volumetric sequences. These moulds allow slicing tumour specimens in identical planes to the MR acquisition and increase the accuracy of tissue sampling. The biopsies will then undergo molecular profiling such as metabolomic and RNA sequencing (including mRNA immune profiling), as well as DNA sequencing to assess driver and clonal mutations in different tumour habitats and guide design of appropriate cfDNA probes. The targeted cfDNA capture panel will be employed to determine the ability of cfDNA to capture the full genetic diversity observed in the primary tumour and to relate cfDNA to various imaging habitats in both renal and pancreatic cancer. Data integration will be undertaken between imaging habitats and molecular profiles for each region.

  Study EGAS00001003703

• Exome sequencing of Congenital Heart Disease families Toronto

  The exome sequencing is performed using Agilent SureSelect 50Mb exome v3 and Hiseq 75bp paired reads with an mean sequencing coverage target of 50X.

  Dataset EGAD00001000799

• Genomic Characterization of Patient-Derived Xenograft Models to Improve Targeted Therapy for HER2+ Breast Cancer Brain Metastases Treatments

  We have developed orthotopic patient-derived xenograft models of HER2 positive breast cancer metastasized into the brain of patients to test novel therapeutic strategies. In this study, we identified a novel combinatorial therapeutic strategy that has resulted in a durable remission and markedly increased overall survival in majority of patient-derived xenograft (PDX) models tested. We performed whole exome sequencing analysis of these PDX tumors and their matched blood and patient samples to investigate drug sensitive and resistance mechanisms. Our sequencing data revealed an interesting association of genotyping and phenotyping with tumors responses to drug treatment.

  Study phs001063

• The Genomic Landscape of Childhood and Adolescent Melanoma

  Despite remarkable advances in the genomic characterization of adult melanoma, the molecular pathogenesis of pediatric melanoma remains largely unknown. We analyzed 15 conventional melanomas (CM), 3 melanomas arising in congenital nevi (CNM), and 5 spitzoid melanomas (SM), using various platforms, including whole genome or exome sequencing, molecular inversion probe assay, and/or targeted sequencing. CM demonstrated a high burden of somatic single nucleotide variations (SNV), with each case containing a TERT promoter (TERT-p) mutation, 13/15 containing an activating BRAF V600 mutation, and >80% of the identified SNV consistent with UV damage. By contrast, the 3 CNM contained an activating NRAS Q61 mutation and no TERT-p mutations. SM were characterized by chromosomal rearrangements resulting in activated kinase signaling in 40%, and an absence of TERT-p mutations except for the one SM that succumbed to hematogenous metastasis. We conclude that pediatric CM has a very similar UV-induced mutational spectrum to that found in the adult counterpart, emphasizing the need to promote sun protection practices in early life and to improve access to therapeutic agents being explored in adults in young patients. By contrast, the pathogenesis of CNM appears to be distinct. TERT-p mutations may identify the rare subset of spitzoid melanocytic lesions prone to disseminate.

  Study EGAS00001000901

• Paired-end RNA-Seq Dataset of 72 Brain Organoid Samples: Sequencing and Gene Expression Analysis

  72 fastq sequencing files of 72 brain-organoid paired-end sequenced samples (R1/R2). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (New England Biolabs, USA). mRNAs were first enriched with Oligo(dT) beads. The samples were sequenced using a 2x150 Pair-End configuration (ver. 1.5) on an Illumina NovaSeq 6000 The raw sequence reads were aligned to the human reference genome GRCh38 using the STAR aligner (Dobin et al., 2013). Gene expression levels were quantified using the FeatureCounts tool (Liao et al., 2014) (file: "All_Counts_final.xlsx") For more information, see "Study Description"

  Dataset EGAD50000000935

• Sequencing data for oesophageal and related samples - Ganguli et al (WGS)

  Data supporting: "TBC" Ganguli et al (WGS for 1298 samples)

  Dataset EGAD00001011191

• SNP genotyping of the HLA and T cell receptor regions

  This dataset contains genotype information (vcf files) for genotyped SNPs within or near (within 1 million bases) the HLA and TCR (TRA and TRB) loci of 187 individuals (98 controls and 89 subjects with coeliac disease). SNPs were genotyped using an Axiom Human Genotyping SARS-CoV-2 Research Array (Thermo Fisher) and the data was processed with the Axiom Analysis Suite using the “Best Practices Workflow” pipeline. The genotyped SNPs include 6791 SNPs within/near the HLA region on Chr6, 685 SNPs within/near TRA on Chr14, and 262 SNPs within/near TRB on Chr7 passing quality control. The dataset also contains a metadata file (csv) describing sample phenotypes and providing links to genotype sample names.

  Dataset EGAD50000002728

• Somatic mutation and clonal evolution in premalignant lung disease

  In this study we aim to characterise the landscape of mutation and clonal selection in normal lung and premalignant lung disease. The study combines targeted sequencing and whole-genome sequencing of microbiopsies of lung and bronchial epithelium. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with premalignant lung disease. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010122

• Genomic Analysis of Extra-Nodal Natural Killer/T-Cell Lymphoma (ENKTCL)

  In this study, we performed extensive genetic profiling on 209 extra-nodal natural killer/T-cell lymphoma (ENKTCL) nasal-type cases, including 174 Chinese from four hospitals in China, and 31 Hispanic and 4 Caucasian patients from City of Hope and Eberhard Karls University of Tübingen. All of the cases were reviewed by experienced hematopathologists to confirm diagnosis. Written informed consents from patients were reviewed and approved by the institutional review board of each institution. We deposited targeted exon sequencing data of a selected 333-gene panel on the ENKTCL cases in dbGaP. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissues with an AllPrep DNA/RNA FFPE Kit. A custom platform (Agilent SureSelect) was used to capture target exons from genomic DNA of ENKTCL tumors. DNA was fragmented to 200bp using a Covaris S220 Focused-ultrasonicator and was end-repaired and ligated to Illumina adaptors with a KAPA Hyper Prep Kit. Ligated products were purified and amplified with a 7-cycle PCR. Exome capture from the PCR products was performed using a SureSelect Target Enrichment Kit. The captured exomes were further amplified with an 8-cycle PCR and purified for cluster generation using the cBot cluster generation system with a HiSeq PE Cluster Kit V4. 100bp paired-end reads were generated from an Illumina HiSeq 2500 system with a HiSeq SBS Kit V4.

  Study phs002925

• AmsterdamUMC Data Access Committee for the study entitled "Carboxylesterase 1 mediates a distinctive metabolic profile of dendritic cells to attain an inflammatory phenotype"

  The current data access committee reviews and assesses data requests of researchers that seek to gain access to data presented in the manuscript entitled "Carboxylesterase 1 mediates a distinctive metabolic profile of dendritic cells to attain an inflammatory phenotype" as performed at the AmsterdamUMC, Amsterdam, Netherlands.

  Dac EGAC50000000178

• LuCaP cell line RNA-seq

  RNA-seq of LuCaP 189.4 cell line. Treatment with DCC DMSO (n=3 replicates) or 1nm R1881 (n=3 replicates). All 6 samples were sequenced using cDNA oligo-dT using paired-end reads on Illumina NovaSeq 6000. Each sample has 2 fastq files, one for the forward and reverse read, respectively.

  Dataset EGAD50000001344

• 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

• HIV-phyloTSI: PANGEA (PCR amplicon)

  This dataset includes sample numbers TSI_0426 to TSI_0527 for the PANGEA (PCR amplicon) cohort of the study. Samples were generated by pooling four overlapping PCR amplicons (see Gall et al 2012, DOI: 10.1128/JCM.01516-12). The sequencing was conducted using the Illumina NovaSeq system. Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001308

• 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

• Set_of_human_mesenchymal_CSA

  51 DNA methylation arrays of human samples initially diagnosed as mesenchymal chondrosarcoma. Microdissection of the cartilage and/or the small round cell component from the same sample may have occurred. As mentioned in the sample descriptions, the diagnoses of four samples have been revised. Additional molecular investigations were conducted for a subset of samples as described in the related publication.

  Dataset EGAD00010002515

• 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

• Oxford Human Islet whole genome bisulphite data of 10 human pancreatic islet samples

  DNA from 10 human pancreatic islet samples was processed for Whole-genome Bisulphite Sequencing. The resulting libraries were sequenced on an Illumina Hiseq 2000 to generate 100bp paired-end read data. The resulting fastq.gz and mapped bam files were deposited.

  Dataset EGAD00001003946

• Whole exome Sequencing (WES) of multiple tumor biopsies, patient-derived spheroids and leukocyte DNA from colorectal cancer patients (BAM files)

  WES was performed using the KAPA-Hyper prep kit from Illumina (Roche, Basel, Switzerland) for library construction, followed by exome capture using Niblegen SeqCap EZ Human Exome Library v3.0 (Roche). Reads were mapped using BWA MEM against the humane reference genome HG19.

  Dataset EGAD00001003821

• Achilles tendinopathy exome data

  Exemplar asymptomatic controls (n=10, 6 males) and exemplar cases with chronic Achilles tendinopathy (n=10, 6 males), representing divergent extremes of the phenotype spectrum were selected for WES. Individual samples were sequenced at paired ends on the Illumina HiSeq 2000/2500 platform at 30X coverage using the Agilent V5+UTR (71Mbp) capture kit.

  Dataset EGAD00001004362

• Ashkenazi Jewish Leukoencephalopathy Syndrome

  Using whole exome sequencing (WES), we identified homozygosity for a missense variant, VPS11: c.2536T>G (p.C846G), as the genetic cause of a leukoencephalopathy syndrome in two individuals from two unrelated Ashkenazi Jewish (AJ) families. Both patients exhibited highly concordant disease progression characterized by infantile onset leukoencephalopathy with brain white matter abnormalities, severe motor impairment, cortical blindness, intellectual disability, and seizures.

  Dataset EGAD00001002005

• Mutational Analysis of Colorectal PDX models (2016-01-06)

  Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2016-01-06.

  Dataset EGAD00001001872

• Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases

  Dataset consisting of three WGS BAM files, representing the two dual lung metastases with matched germline control, for a 37 year old female patient, with primary adrenocortical carcinoma. Work conducted at Garvan Institute of Medical Research, Sydney, Australia.

  Dataset EGAD00001004833

• RNA-seq TPM matrices

  Matrices of TPM-normalized counts from RNAseq data for the three phase II clinical trials (IMvigor210, POPLAR, IMmotion150) and the phase I clinical trial PCD4989g.

  Dataset EGAD00001006741

• Small RNA sequencing from CSF extracellular vesicles - PD/CTR

  The dataset contains FASTQ files referring to the study "Small RNA sequencing from CSF extracellular vesicles - PD/CTR". For this project, RNA was isolated from CSF extracellular vesicles obtained by ultracentrifugation. Libraries were prepared with the TruSeq Small RNA library prep Illumina, and sequencing conducted in the Illumina HiSeq4000.

  Dataset EGAD00001006629

• Whole genome sequencing of GM09237 cells with and without folate depletion

  Two DNA samples extracted from GM09237 cell line cultured with either normal medium or medium with no folic acid for 5 days were sequenced using the BGISEQ500 platform (BGI whole genome 100 bp paired-end sequencing 60x) as well as PacBio Sequel long read sequencing.

  Dataset EGAD00001007732

• 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

• Single cell epigenomic study of H3-K27M mutant diffuse midline glioma across age and location

  This dataset contains the open chromatin profiles of 8 patient H3-K27M mutant DMGs utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

  Dataset EGAD00001010170

• Germline genome sequencing samples from the Hereditary Cancer Syndromes (ICCon) Cancer Flagship

  A prospective study of individuals with suspicion of a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or was not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing and a comprehensive cancer virtual gene panel analysis were undertaken.

  Dataset EGAD00001011260

• COVID-19 Multiomics Atlas

  We provide a single-nuclei RNA-sequencing (snRNA-seq) dataset derived from four COVID-19 patients, generated using the 10x Chromium Next GEM Single Cell v3.1 kit. For our study, these were integrated with snRNA-seq data with 12 publicly available sc/snRNA-seq datasets, comprising organ donor lung samples (n=89) and COVID-19 lung tissue samples (n=51).

  Dataset EGAD00001015602