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• Gene expression in human monocyte differentiation

  This dataset consists of RNA-seq data data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting TET2, IRF4 and EGR2. In total, it includes 43 samples.

  Dataset EGAD00001006604

• Mutational signatures in esophageal squamous cell carcinoma from eight countries of varying incidence – sequence data (Mutographs)

  Mutational signatures in esophageal squamous cell carcinoma from eight countries of varying incidence – sequence data (Mutographs)

  Dataset EGAD00001006868

• Transcriptome analysis of Treg cells from blood, fat, liver and skin

  Tcells were isolated fom Tissues and FACS sorted. In total 43 samples were processed in 5 replicates with the Takara SmartSeq Stranded kit. Single end fastq-files are supplied.

  Dataset EGAD00001007664

• CLL2 dataset used in FLTseq paper

  This dataset contains CLL2 data used in FLTseq paper. The dataset contains the data of CITEseq, FLTseq, RaCHseq, Exonseq and bulk RNAseq.

  Dataset EGAD00001008114

• Gene expression in LPS-stimulated human monocyte-derived macrophages

  This dataset consists of RNA-seq data from human monocyte-derived macrophages that were subjected to siRNA treatment targeting RAD21 and either left untreated, or stimulated with LPS. In total, it includes 24 samples.

  Dataset EGAD00001007952

• Molecular determinants of outcomes in relapsed mantle cell lymphoma treated with ibrutinib or temsirolimus in the MCL3001 (RAY) trial

  234 BAM files containing capture data of MCL tumours and constitutive DNA

  Dataset EGAD00001008975

• Exome Sequencing of 44 subjects with very severe or fatal COVID-19

  In this study, the DNA of 44 subjects with severe COVID-19 have been sequenced in order to explore rare genetic variants.

  Dataset EGAD00001008993

• Mutation analysis of 77 genes in cfDNA from metastatic CRC patients

  Aligned NGS data (BAM) of 77 frequently mutated genes in cancer using the AVENIO Expanded platform.

  Dataset EGAD00001010294

• Reference epigenomes generated as part of the International Human Epigenomics Consortium (IHEC)

  The Centre for Epigenome Mapping Technologies (CEMT) is an epigenome sequencing platform funded by the Canadian Institutes of Health Research (CIHR) and Genome BC as part of the Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC). CEMT aims to produce 100 human reference epigenomes, each comprising the following datasets: whole genome; whole genome bisulfite and oxidative bisulfite; transcriptome; microRNA; and chromatin immunoprecipitation (ChIP)-seq for the core chromatin marks (H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K36me3, and H3K27ac).CEEHRC is a full member of the International Human Epigenomics Consortium (IHEC), which aims to coordinate the production of 1,000 reference maps of human epigenomes for key cellular states relevant to health and diseases. As such, all datasets submitted by the CEMT platform conform to IHEC assay standards and metadata guidelines.

  Study EGAS00001000552

• Molecular Subtype-specific Biomarkers Improves Colorectal Cancer Prognostication

  Colorectal cancer (CRC) is characterized by major inter-tumor diversity that complicates the prediction of disease and treatment outcomes. Recent efforts help resolve this by sub-classification of CRC according to natural molecular subtypes, however, this strategy is not yet able to provide clinicians with improved tools for decision-making. We here present an extended framework for CRC stratification that specifically aims to improve patient prognostication. Using transcriptional profiles from 1,100 CRCs, including a novel set of >300 samples, we identify novel cancer cell and tumor archetypes and suggest the tumor microenvironment as a major prognostic determinant that can be influenced by the microbiome. Notably, our subtyping strategy allowed identification of novel archetype-specific prognostic biomarkers that provided information beyond and independent of UICC-TNM staging, MSI-status and consensus molecular subtyping. The results illustrate that our extended subtyping framework, combining subtyping and subtype-specific biomarkers, could contribute to improved patient prognostication and may form a strong basis for future studies.

  Study EGAS00001002376

• Khoe-San genome Project (KSGP)

  The Khoe-San Genome Project (KSGP) includes whole genome data generated for 190 study participants from Southern Africa (Namibia and South Africa) representing people speaking a Namibian Khoe-San language (n=150, 12 groups) or regional non-Khoe-San groups (n=40), specifically defined here as Namibian Himba (n=10), South African Southern Bantu (n=12 and representing the Ubuntu Genome Project led by the University of Limpopo) or South African Coloured/European (n=18). Deep whole genome data has been generated for the purposes of cataloguing the extent of regional genetic diversity, creating population specific references and evolutionary trajectories, while creating a population-matched panel of normal (PoN) genetic diversity required for disease associated studies across the region.

  Dac EGAC50000000798

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (healthy cell_line)

  Dataset EGAD00001003283

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

  Data supporting: "Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma." Noorani et al. WGS (BAM files) 134 samples for 18 cases Includes primary, lymph-node, distant metastatic, Barrett's and normal samples.

  Dataset EGAD00001005434

• Dichotomous regulation of lysosomes by MYC and TFEB controls hematopoietic stem cell fate

  We show that lysosomes are antagonistically controlled by TFEB and MYC to balance catabolic and anabolic processes required for activating LT-HSC and guiding their lineage fate. TFEB-mediated induction of the endolysosomal pathway for membrane receptor degradation limits LT-HSC metabolic and mitogenic activation; this promotes quiescence and self-renewal and governs erythroid-myeloid commitment. By contrast, MYC engages biosynthetic processes while repressing lysosomal catabolism to drive LT-HSC activation. Collectively, our study identifies lysosomes as a central regulatory hub for proper and coordinated stem cell fate determination.

  Dataset EGAD00001006884

• A Phase I Study with a Personalized Neoantigen Cancer Vaccine in Melanoma

  Effective anti-tumor immunity in humans has been associated with presence of T cells targeting neoantigens that arise from non-silent tumor-specific mutations. Here we conducted whole-exome sequencing of tumor and normal cells from individual patients to identify mutations. We assessed the expression of mutated alleles by RNA-sequencing of tumor. We demonstrated the feasibility, safety and immunogenicity of a vaccine that targets up to 20 personal neoantigens predicted to be presented by the autologous patient tumor.Antigen-specific CD8+ T cells that can recognize and eliminate cancer cells play a crucial role in anti-tumor immune responses. Here we conducted single-cell sequencing of cells infiltrating melanoma specimens originating from 4 patients and determine the TCR clonality of the CD8+ tumor infiltrating cells. We investigated the relationship between T cell clonality and phenotypic cell states coupling single-cell transcriptome to single-cell TCR seq. The surface expression of a panel of protein was detected in parallel using CITE-Seq antibodies. Sorted tumor and peripheral blood specimens were processed in parallel.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out matched ribosome profiling (Ribo-seq), RNA-sequencing, and whole genome sequencing on one of the patients, as well as Ribo-seq on an additional patient. We used it to discover novel or unannotated open reading frames (nuORFs), their expression levels, as well as somatic mutations within them to predict potential neoantigens.

  Study phs001451

• Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis

  Targeted therapy interventions using tyrosine kinase inhibitors (TKIs) provide encouraging treatment responses in ALK-rearranged lung adenocarcinomas, yet resistances occur almost inevitably. Apart from tumor cell-intrinsic resistance mechanisms, accumulating evidence supports a role of cancer-associated fibroblasts (CAFs) in affecting the therapeutic vulnerability of lung cancer cells. Here, we aimed to investigate underlying molecular networks shaping the therapeutic susceptibility of ALK-driven lung adenocarcinoma cells via tumor microenvironmental cues using three-dimensional (3D) spheroid co-culture settings. We show that CAFs promote therapy resistance of lung tumor cells against ALK inhibition by reducing apoptotic cell death and increasing cell proliferation. Using single-cell RNA-sequencing analysis, we show that genes involved in lipogenesis constitute the major transcriptional difference between TKI-treated homo- and heterotypic lung tumor spheroids. CAF-conditioned medium and CAF-secreted factors HGF and NRG1 were both able to promote resistance of 3D-cultured ALK-rearranged lung tumor cells via AKT signaling, which was accompanied by enhanced de novo lipogenesis and supression of lipid peroxidation. Notably, simultaneous targeting of ALK and SREBP-1 was able to overcome the established CAF-driven lipid metabolic-supportive niche of TKI-resistant lung tumor spheroids. Our findings highlight a crucial role of CAFs in mediating ALK-TKI resistance via lipid metabolic reprogramming and suggest new ways to overcome resistance towards molecular directed drugs by targeting vulnerabilities downstream of oncogenic signaling.

  Study EGAS50000000135

• Initial whole genome sequencing of plasma cell neoplasms in First Responders exposed to the World Trade Center attack of September 11, 2001

  The World Trade Center (WTC) attack of September 11, 2001 created an unprecedented environmental exposure to known and suspected carcinogens. High incidence of multiple myeloma (MM) and precursor conditions has been reported among first responders to the WTC disaster. To expand on our prior screening studies, and to characterize the genomic impact of the exposure to known and potential carcinogens in the WTC debris, we were motivated to perform whole genome sequencing (WGS) of WTC first responders and recovery workers who developed a plasma cell disorder after the attack. PATIENTS AND METHODS: We performed WGS of 9 CD138-positive bone marrow mononuclear samples from patients who were diagnosed with plasma cell disorders after the WTC disaster. RESULTS: No significant differences were observed in comparing the post-WTC driver and mutational signatures landscape with 110 previously published WGS from 56 patients with MM and the CoMMpass WGS cohort (n=752). Leveraging constant activity of the single base substitution mutational signatures 1 and 5 over time, we estimated that tumor-initiating chromosomal gains were windowed to both pre- and post-WTC exposure. CONCLUSIONS: Although limitations in sample size preclude any definitive conclusions, our findings suggest that the observed increased incidence of plasma cell neoplasms in this population is due to complex and heterogeneous effects of the WTC exposure that may have initiated or contributed to progression of malignancy.

  Study EGAS00001004467

• The Genetic Landscape of Mutations in Burkitt Lymphoma

  Burkitt lymphoma (BL) is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. We sequenced exomes of 59 BL tumors, 14 of which had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a novel tumor suppressor gene.

  Study phs000562

• Determinants of Asthma Following RSV Bronchiolitis in Early Life

  The goal of the RSV Bronchiolitis in Early Life (RBEL) study is to determine how specific genetic, biologic, and immunologic characteristics interact to predispose individuals to develop asthma. Participants were carefully recruited by selecting a prospective cohort of 206 infants with severe respiratory syncytial virus (RSV) bronchiolitis who were at substantial risk of developing asthma.

  Study phs001009

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778

• Identifying and Reducing Disparities in Patient-Reported Outcomes Among African American Prostate Cancer Survivors

  This research study aimed to identify disparities in prostate cancer symptom burden and their contributors among African American, Hispanic, and non-Hispanic White prostate cancer survivors. We collected patient-reported outcomes data, focusing on various aspects of the survivors' health and well-being, clinical data, demographics data, and germline genomic data.

  Study phs003745

• Immune Landscape of Cervical Lymph Nodes in Multiple Sclerosis

  This study aimed to investigate the cellular compartment of deep cervical lymph nodes (dcLNs) during early MS before the influence of immunosuppressive treatments. We used ultrasound-guided FNAs followed by scRNA-seq,CITE-seq, TCR and BCR seq to characterize the immune landscape in MS patients compared to controls within the dcLNs.

  Study EGAS50000000843

• Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  PPM1D, a central regulator of the DNA damage response, is commonly mutated in therapy-related clonal hematopoiesis (CH), acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). PPM1D mutations have been shown to expand under selective pressure of DNA-damaging chemotherapy. However, whether PPM1D mutations promote the development of hematologic malignancies remains unclear.

  Study EGAS50000000840

• Single nucleus and bulk transcriptomics in prefrontal cortex of individuals with alpha synucleinopathies

  We explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single nucleus RNA sequencing using 10X Genomics, and bulk RNA sequencing from the prefrontal cortex of individuals with alpha synucleinopathies - Parkinson's Disese (PD), monogenic LRRK2 PD, and multiple system atrophy (MSA), together with neurologically healthy controls.

  Study EGAS50000000301

• Transcriptomic analysis of hiPSC-derived vascular cells from CADASIL and isogenic control patient lines

  Bulk-RNA sequencing from hiPSC-derived cells (hiPSC; Endothelial Cells; Neural Crests Cells; Vascular Smooth Muscle Cells) from CADASIL patient lines (n=3) and respective isogenic-controls (n=3). CADASIL is a hereditary brain small vessel disease caused by pathogenic variants in the NOTCH3 gene, which lead to deposits of NOTCH3 protein in the walls of small arteries. This causes pathological vessel wall changes including degeneration of vascular smooth muscle cells. To investigate the impact of pathogenic NOTCH3 variants in hiPSC and differentiated cells we performed a bulk-RNA sequencing.

  Dataset EGAD50000002181

• RNA sequencing data of pediatric T-cell acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one T-ALL patient (ALLK-118) and from a relapse sample from bone marrow of one T-ALL patient (ALLT-317). Data from the diagnostic sample and relapse sample from tonsil of the ALLT-317 patient are in set 2 of this submission. TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic and relapse tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002584

• Defective mitophagy and enhanced oxidative stress dictate regulatory T cell impairment in autoimmunity

  Regulatory T cell (Treg) impairment is a common denominator of autoimmune pathologies. Despite the extensive characterization of Treg cell phenotype in autoimmunity, the molecular mechanisms underlying their deterioration remain ill defined. To investigate Treg dysfunction during autoimmunity we performed transcriptomic analysis of CD4+CD25highCD127- Treg cells from peripheral blood of patients with autoimmunity.

  Study EGAS00001004470

• Identification of molecule relationship between intravenous leiomyomatosis and uterus myoma

  Up to now, there are two hypothesis about the pathogenesis of the relationship of intravenous leiomyomatosis and uterine myoma. One theory suggests that the IVL comes from the smooth muscle cell in the vessel wall.The other theory indicates that the IVL derives from the uterine myometrium. However, limited to the technology, few studies have been deeply explore the underlying relation. In this study, we employ the RNA sequencing to explore the molecule relationship between IVL and uterus myoma. In order to identify the molecule relationship between IVl and uterine myoma we conducted transcriptome sequencing and bioinformaitc analysis

  Dataset EGAD00001003356

• The WID-BC-index identifies women with primary poor prognostic breast cancer based on DNA methylation in cervical samples

  A surrogate marker based on the epigenome that captures these components in easily accessible epithelial tissue could potentially identify women at risk. The WID-BC-index identifies women with breast cancer based on a DNA methylation signature derived from cervical smear samples.

  Study EGAS00001005055

• Chordoma Sequencing Project Whole Genome

  This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

  Dataset EGAD00001000721

• Whole-genome plasma DNA sequencing in CRC patients under anti-EGFR therapy

  In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy.

  Dataset EGAD00001000748

• Whole Genome Sequencing of CRLF2/IL7RA transduced cells

  There are two samples, 42 (control) and 49 To test the role of activated CRLF2/IL7RA in leukemia initiation we expressed CRLF2 together with IL7RA in human CB hematopoietic progenitors. Human CRLF2 and wild type and/or activated mutant form of human IL7RA (IL7RAwt/ins) were cloned into a lentiviral vector with a bi-cistronic cassette under the expression control of an Eμ-B29 promoter/enhancer to augment expression in B-cell precursors. Backbone vector expressing GFP (BB). Whole genome sequencing Leukemic (49) and BB transduced (42) corresponding CB cells were collected from transplanted mice. Sequencing libraries were prepared from these samples

  Dataset EGAD00001005456

• Targeted Germline Sequencing of the Leeds Melanoma Cohort

  In this project we performed targeted sequencing of known and suspected melanoma susceptibility genes in a cohort of melanoma patients and matched controls. Our aim was to identify variants that predispose to melanoma development. The melanoma cases used in this study were population ascertained.

  Dataset EGAD00001007520

• Targeted NGS panel

  The mutational status of 121 genes recurrently altered in B-cell lymphoma was examined in 55 of 56 diagnostic and 10 of 12 relapse samples using a custom targeted NGS panel. Libraries were generated from 150 ng of DNA using molecular-barcoded library adapters (ThruPLEX Tag- seq kit; Takara) coupled with a custom hybridization capture-based method (SureSelectXT Target Enrichment System Capture strategy, Agilent Technologies). The quality of the libraries was determined using the Bioanalyzer high sensitivity DNA kit (Agilent) and quantified by PCR using the KAPA library quantification kit (KAPA Biosystems). Finally, the libraries were pooled and sequenced in the MiSeq instrument (Illumina).

  Dataset EGAD00001010842

• Exome Chip Study of NIMH Controls

  Here, we report exome chip genotyping results of 1052 samples from the NIMH control set, a collection of healthy controls for general research use. The samples are all unrelated.

  Study phs000630

• RGB TGCT Data Access Committee

  The RGB TGCT Data Access Committee is responsible for reviewing and approving requests for access to controlled genomic data generated from testicular germ cell tumor (TGCT) patients treated at the National Cancer Institute of Mexico (INCan). The committee evaluates requests to ensure that data use complies with the informed consent provided by participants and with applicable institutional and ethical regulations.

  Dac EGAC50000000959

• Genomewide Association Study of Inflammatory Bowel Disease

  WTCCC genome-wide case-control association study for Inflammatory Bowel Disease (IBD) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000006

• RNA-sequencing of ex situ stimulated donors blood cells

  Cells from whole blood stimulation assay were cryopreserved. The cryopreserved cells were thawed and subjected to RNA preparation. RNA obtained were subjected to for bulk sequencing.

  Study EGAS50000001077

• GBM Study Complete Raw Data

  Tumors from 173 GBM patients were analysed for somatic mutations to generate a personalized peptide vaccine targeting tumor-specific neoantigens. Exome libraries for 173 glioblastoma tumors and matched normal DNA were sequenced on Illumina platform, alongside total RNA from the tumors.

  Dataset EGAD50000000650

• Human TRIM24-MET fusion HGG RNA-seq

  Human RNA-seq data for TRIM24-MET fusion tumor primary samples and patient/PDOX-derived cell lines. Cells were treated with 0.1% DMSO or EC90 of MET inhibitors (capmatinib, cabozantinib, crizotinib) for 4 hours. BAM files containing aligned (and unaligned) reads to hg19 are provided.

  Dataset EGAD50000000194

• RNA-Seq data of S24 cells for the publication Recording physiological history of cells with chemical labeling.

  Recordings of elevated calcium levels allowed selections of cells from heterogenous populations for transcriptomic analysis. Paired RNA-Seq from S24 cells using Takara SMARTer Ultra Low Input RNA v4 kit and sequencing on a Illumina NovaSeq 6000.

  Dataset EGAD50000000082

• WGS dataset for gamma delta (γδ) T-ALL patients

  Whole genome sequencing data for 61 samples with acute lymphoblastic leukemia expressing the gamma delta T cell receptor (γδ T-ALL) and 29 germline samples

  Dataset EGAD50000000028

• Array data for oesophageal and related samples – sj_paper_methyl_tumour_release

  Array data for oesophageal and related samples – sj_paper_methyl_tumour_release

  Dataset EGAD00010001822

• TenK10K Phase 1: snATAC-seq FASTQ files

  Raw FASTQ files for single cell ATAC-sequencing data for PBMCs from the Tenk10k Phase 1 cohort (952 individuals pre-QC). Libraries were prepared using the 10x Genomics Chromium Next GEM Epi ATAC v2 kit and sequenced on the NovaSeq 6000 platform.

  Dataset EGAD50000002682

• Chromatin_Profiling_in_Twins

  50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, subjected to Chromatin Immunoprecipitation using an antibody for H3K4me1. H3K4me1 peaks mark distal regulatory elements.

  Study EGAS00001000098

• Myeloma_Targeted_Follow_up_Study

  390 samples, perform WGA, and send the WGA’d DNA to core for pre-capture library and tagging, pulldown with ELID 631172 (16 samples per reaction tube), and sequencing (24 samples per lane)

  Study EGAS00001000880

• BIG_MS_Pilot

  Testing logistics and infrastructure of molecular screening program. Core biopsies taken from invasive recurrent or metastatic breast cancer to evaluate and identify molecular traits rendering them suitable for clinical trials

  Study EGAS00001000616

• SureTypeSC - accurate genotyping of single-cell SNP array data

  We used a collection of single cells from two Coriell cell lines to train and validate a machine learning method for quality assessment of the single cell genotypes

  Study EGAS00001004621

• Epi2Diag raw methylation array data for patients with neurodevelopmental disorders

  Raw methylation array data (Illumina Infinium EPIC v2.0) from patients with rare neurodevelopmental disorders. IDAT files were generated from DNA extracted from whole blood at the ASGARD platform, Inserm U1245, Univ Rouen, CHU Rouen, to investigate new episignatures and provide independent validation datasets for existing episignatures.

  Dataset EGAD00010002724

• Characterization of iPSC derived macrophages - cardiovascular pilot (2017-05-24)

  This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-05-24.

  Dataset EGAD00001003347

• WES fastq files of IPDGC UK cohort

  As part of the International Parkinson's Disease Genomics Consortium, exomes of Parkinson's disease (PD) patients and healthy controls were sequenced to study the genetic etiology of PD. This UK cohort consists of 70 PD patients. Researchers can apply for access to fastq files for this cohort.

  Dataset EGAD00001003096

• Next generation sequencing of liver cancer cell lines

  Whole genome sequencing was performed for 81 liver cancer cell lines. Additional whole exome sequencing was performed for a subset of 11 liver cancer cell lines. SK_HEP_1 was also provided, though considered not hepatic origin. These sequencing data provided the detailed genomic characterization of liver cancer models.

  Dataset EGAD00001003165

• WGS files for Mullighan PAX5_B-ALL

  WGS files for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"

  Dataset EGAD00001004446

• WES files for Mullighan PAX5_B-ALL

  WES files for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"

  Dataset EGAD00001004447

• Diffuse Intrinsic Pontine Glioma

  This study contains DNA and RNA sequencing data for 5 DIPG patients. All patients have tumor DNA data, 4 have matched normal DNA data and 3 have tumor RNA seq data

  Study EGAS00001006353

• Prediction of HLA genotypes using NGS data

  High-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate.

  Study EGAS00001005274

• Microinjection of hIPSC-derived intestinal organoids with Salmonella Typhimurium

  To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001001363

• BLUEPRINT release August 2015, RNA-Seq for Multiple myeloma, on genome GRCh38

  RNA-Seq data for 11 Multiple myeloma sample(s). 11 run(s), 11 experiment(s), 11 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001471

• BLUEPRINT release August 2015, DNase-Hypersensitivity for Acute Myeloid Leukemia, on genome GRCh38

  DNase-Hypersensitivity data for 1 Acute Myeloid Leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820

  Dataset EGAD00001001549

• BLUEPRINT release January 2015, DNase-Hypersensitivity for inflammatory macrophage

  DNase-Hypersensitivity data for 2 inflammatory macrophage sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001193

• BLUEPRINT release August 2015, RNA-Seq for monocyte, on genome GRCh38

  RNA-Seq data for 4 monocyte sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001572

• BLUEPRINT: RNA-seq for monocytes and neutrophils

  RNA-seq for monocytes and neutrophils

  Dataset EGAD00001000675

• BLUEPRINT: ChIP-seq for monocytes & neutrophils

  ChIP-seq for monocytes and neutrophils

  Dataset EGAD00001000676

• BLUEPRINT release August 2014, DNase-Hypersensitivity for inflammatory macrophage

  DNase-Hypersensitivity data for 2 inflammatory macrophage sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000926

• BLUEPRINT release August 2016, DNase-Hypersensitivity for macrophage - T=6days untreated, on genome GRCh38

  DNase-Hypersensitivity data for 4 macrophage - T=6days untreated sample(s). 6 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002398

• BLUEPRINT release August 2016, DNase-Hypersensitivity for monocyte - T=0days, on genome GRCh38

  DNase-Hypersensitivity data for 2 monocyte - T=0days sample(s). 4 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002300

• BLUEPRINT release August 2016, DNase-Hypersensitivity for macrophage - T=6days LPS, on genome GRCh38

  DNase-Hypersensitivity data for 4 macrophage - T=6days LPS sample(s). 6 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002290

• BLUEPRINT release August 2016, DNase-Hypersensitivity for Chronic Lymphocytic Leukemia, on genome GRCh38

  DNase-Hypersensitivity data for 2 Chronic Lymphocytic Leukemia sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002459

• BLUEPRINT release August 2016, DNase-Hypersensitivity for Acute Myeloid Leukemia, on genome GRCh38

  DNase-Hypersensitivity data for 37 Acute Myeloid Leukemia sample(s). 38 run(s), 37 experiment(s), 37 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002355

• Clinical phenotypes/covariates

  This dataset contains the clinical phenotypes/covariates information for all the individuals. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005040

• CRISPR screen M14, NCI-H3122 (2019-08-28)

  Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung . This dataset contains all the data available for this study on 2019-08-28.

  Dataset EGAD00001005296

• WGBS for T-Cell and B-Cell, control and tumor

  WGBS data for 75 paired fastq, spread over 31 samples (4 healthy T-cell, 7 healthy B-cell, 20 B-cell CLL tumors) of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005970

• A95673A

  Whole genome sequencing for single cells for library A95673A 1446 cells; filetype=bam

  Dataset EGAD00001006941

• A96217B

  Whole genome sequencing for single cells for library A96217B 1616 cells; filetype=bam

  Dataset EGAD00001006945

• A98269B

  Whole genome sequencing for single cells for library A98269B 1609 cells; filetype=bam

  Dataset EGAD00001006947

• CITE-seq for peripheral blood samples of 5 breast cancer patients

  We have 5 breast cancer patients who received VEN therapy. We collected their peripheral blood samples before and after long-term Venetoclax treatment. We apply CITE-seq protocol to these samples. This collection contains the all CITE-seq data for patients.

  Dataset EGAD00001008751

• RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 10) or with vehicle (N = 10).

  Dataset EGAD00001009389

• Sequencing data for oesophageal / related samples - Kazachenka et al (RNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" RNAseq for 279 samples

  Dataset EGAD00001011076

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

  Data supporting: "TBC" Ganguli et al (sWGS for 75 samples)

  Dataset EGAD00001011189

• Sequencing data for oesophageal and related samples - Abbas et al (RNA)

  Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (RNA for 197 samples)

  Dataset EGAD00001011269

• Mapping of runs back to samples for snRNASeq data

  Mapping of runs back to samples for PDN, PDO and TIS snRNASeq data. 4 sets of matched PDN, PDO and TIS samples (12 unique samples total) underwent pooled snRNASeq (Parse Biosciences). 2 sublibraries were created from this and sequenced at separate times

  Dataset EGAD00001015609

• DNA WGS BAM files for PMID: 41845530 titled: Multi-omics reveals key molecular and cellular features of advanced small cell lung cancers associated with distinct therapeutic opportunities

  DNA WGS BAM files for PMID: 41845530 titled: Multi-omics reveals key molecular and cellular features of advanced small cell lung cancers associated with distinct therapeutic opportunities

  Dataset EGAD00001016147

• Single-Cell Analysis of CD19-Specific CAR T Cell Treatment of Relapsed/Refractory CD19+ Acute Lymphoblastic Leukemia

  By leveraging single-cell transcriptome and T cell receptor (TCR) sequencing, we aimed to track the transcriptional signatures of chimeric antigen receptor (CAR) T cell clonotypes throughout the course of treatment and furthermore identify molecular patterns leading to potent CAR T cell cytotoxicity. The data presented in this study encompass blood and bone marrow samples from patients ≤ 21 years of age with relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) participating in the SJCAR19 phase I/II clinical trial (NCT03573700). In brief, patients enrolled in the clinical trial received either 1 x 10^6 (dose level 1) or 3 x 10^6 (dose level 2) per kilogram of body weight following successful generation of autologous CAR T cell products and lymphodepleting chemotherapy. Peripheral blood was drawn from each participant every week until week 4 post-infusion, at week 6 or 8, and month 3 or 6 if feasible. At week 4 post-infusion, blood marrow was also collected from participants. Total T cells (CD3+) were sorted from each post-infusion sample, as well as the pre-infusion CAR T cell products, and processed through 10x Genomics’ single-cell gene expression and V(D)J sequencing platform using the standard protocol. We identified a unique and unexpected transcriptional signature in a subset of pre-infusion CAR T cells that shared TCRs with post-infusion cytotoxic effector CAR T cells. Functional validation of cells with even a subset of these pre-effector markers demonstrated their immediate cytotoxic potential and resistance to exhaustion. The data deposited into dbGaP include all raw single-cell expression and V(D)J sequencing generated from samples obtained from 16 study participants.

  Study phs002966

• METABRIC

  The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (CNVs, SNPs) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, although the landscape was dominated by cis and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP, and MAP2K4. Unsupervised analysis of paired DNA/RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, ER-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration 0152hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the 0152CNA-devoid sub-group and a Basal-specific chromosome 5 deletion-driven mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic copy number aberrations on the transcriptome.

  Study EGAS00000000083

• Clinical and Genetic Analysis of Costa Rican Patients with Parkinson's Disease

  This study is a pilot study designed to describe the clinical and genetic landscape of Parkinson's disease in Costa Rica. While most genetic studies have been conducted on Europeans, few have examined Parkinson's disease in Costa Ricans. 118 patients and 97 controls were recruited at the Movement Disorders Unit of the Department of Neurology, Hospital San Juan de Dios, Caja Costarricense de Seguro Social, Costa Rica. Familial Parkinson's disease genes were sequenced using Next-Generation Sequencing. We also measured and obtained different sociodemographic and clinical information.

  Study phs002495

• Cancer Genetic Markers of Susceptibility (CGEMS) Prostate Cancer Genome-Wide Association Study (GWAS) - Primary Scan (Stage 1) - PLCO Screening Trial

  The Cancer Genetic Markers of Susceptibility (CGEMS) prostate cancer genome-wide association study (GWAS) included genotyping approximately 550,000 SNPs (Phase 1A with HumanHap300 and Phase 1B HumanHap240, both from Illumina, San Diego, CA) in 1,172 prostate cancer patients and 1,157 controls of European ancestry from the Prostate, Lung, Colon and Ovarian (PLCO, http://www.cancer.gov/prevention/plco/) Cancer Screening Trial. The original analysis published in Nature Genetics [PMID: 17401363] included 2,282 subjects. After improvement and revisions of the original analysis, 2,252 subjects were submitted to dbGaP.

  Study phs000207

• Whole exome sequencing of 184 unrelated subjects with 22q11.2 deletion syndrome (DiGeorge syndrome/velo-cardio-facial syndrome)

  Our goal is to find genetic modifiers of major phenotypes in patients with 22q11.2 deletion syndrome, also known as DiGeorge syndrome or velo-cardio-facial syndrome. Whole exome sequencing was performed as part of a contract to the NHLBI, Resequencing and Genotyping Service. We have obtained cardiac phenotype information from the de-identified subjects enrolled in the study, either by echocardiography report or medical doctor report. All of the subjects have a 3 million base pair 22q11.2 deletion flanked by low copy repeats, LCR22, A-D.

  Study phs000987

• Next Generation Mendelian Genetics: Ehlers-Danlos Syndrome Type VIII

  The NHGRI Next Generation Mendelian Genetics project uses exome resequencing to identify variants in unsolved Mendelian diseases. Ehlers-Danlos syndrome Type VIII is a dominantly inherited connective tissue disorder that is distinguished from other forms of EDS by significant early-onset periodontal disease. Although the clinical phenotype is well delineated, the underlying molecular basis remains unknown. By studying a large family of affected and unaffected individuals with the EDS VIII by exome sequencing, we hope to identify unique regions of homology to assist in identifying the causative gene.

  Study phs000540

• Germline Genome Sequencing from Patients with Early-Onset Merkel Cell Carcinoma

  Merkel cell carcinoma (MCC) is a rare neuroendocrine skin cancer associated with advanced age. Approximately 5% of cases are early-onset MCC, occurring in individuals younger than 50 years. This study used genome sequencing to identify germline risk factors among patients with early-onset MCC. The available data in the database of Genotypes and Phenotypes (dbGaP) includes genome sequencing of peripheral blood mononuclear cell (PBMC) DNA from 37 patients with early-onset MCC (age ATM = 2, BRCA1 = 2, BRCA2 = 1, TP53 = 1, and MAGT1 = 1).

  Study phs003485

• Impact of Chemotherapy on the Somatic Mutation Burden of Sperm and Other Tissues

  We applied high-fidelity duplex sequencing to 94 samples from 36 individuals exposed to diverse chemotherapies along with 32 controls. We found that in many of the sperm samples from men exposed to chemotherapy, the somatic mutation burden was elevated compared to controls as well as the expected burden based on trio studies. We then validated this finding using other tissues, and also found increased somatic mutation burden in the blood and liver of many subjects exposed to chemotherapy compared to unexposed controls.

  Study phs003476

• NHLBI TOPMed: African American Sarcoidosis Genetics Resource

  This study aims to comprehensively interrogate the genomes of African American sarcoidosis families. Sarcoidosis is characterized by a hyperimmune response resulting in granuloma formation in multiple organs. It affects African Americans (AAs) more frequently and more severely than whites. While previous linkage, admixture, candidate gene and genome-wide association (GWA) studies show statistically compelling effects, causal variants are still unknown and much of sarcoidosis heritability is yet to be explained. This "missing" heritability likely includes effects of both common (minor allele frequency (MAF)>5%) and rare variants (MAF

  Study phs001207

• Impact of Mutated CTCF DNA binding sites of Topologically associating domains on nearby Cancer Gene Regulation: A Multi-Omics Analysis

  Cutaneous squamous cell carcinoma (cSCC) is the most common lethal malignancy world-wide. Due in most part to the extremely high mutational burden (TMB) in cSCC, making sense of it’s non-coding and regulatory regional genomic variation has lagged that of other far less common cancers. This study presents the first investigation of mutations at CCCTC-binding factor binding sites (CTCFbs) of Topologically associating domains (TAD) across defined cSCC progression stages—primary non-metastatic (PNM), primary metastat-ic (PM), and lymph node metastasis (LNM).

  Study EGAS50000001686

• RNA-seq of MPNSTs

  Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are highly aggressive soft-tissue sarcomas with a poor prognosis and a lack of therapeutic options. In this study, we analyse the whole-transcriptome MPNST and combine them with WGS data from a partially overlapping sample set. These analyses and the inclusion of another public dataset allow us to identify three genomic MPNST subgroups with distinct biological and clinicopathological features that can inform management and precision treatments. Published in "Identification of Malignant Peripheral Nerve Sheath Tumor (MPNST) subtypes with distinct genomic identities."

  Study EGAS50000001733

• Whole exome sequencing of pediatric soft tissue sarcoma PDX models

  Childhood cancer remains one of the leading causes of death in pediatric patients in Europe. Pediatric sarcomas, comprising soft tissue sarcomas and malignant bone tumors, are a heterogenous group of malignancies, with more than 50 subtypes (WHO classification). Due to low case numbers, studying pediatric sarcomas requires accurate and reliable preclinical models. Here, we established 18 soft tissues sarcoma PDX models, including Ewing Sarcoma, Rhabdmyosarcoma and Osteosarcoma. We characterized these models by Whole Exome Sequencing and assessd the response to a wide range of drugs.

  Study EGAS50000000048

• Single-cell Analysis of Neoplastic Plasma Cells Identifies Novel Myeloma Pathobiology Mediators and Potential Targets

  Newly diagnosed symptomatic and relapsed/refractory myeloma is a clonal plasma cell (PC) dyscrasia that arises from precursors which have been studied utilizing bulk or single-cell (sc) techniques. By combining scRNA-sequencing with scB-cell receptor (BCR)-sequencing, we found more dysregulated genes in monoclonal PCs compared with analyses of the entire CD138+ population, which includes non-neoplastic/polyclonal PCs. We identified a panel of genes that were over- or under-expressed in symptomatic states that could be putative oncogenic drivers or tumor suppressors, respectively.

  Study EGAS50000000803

• Encompassing view of spatial and single-cell RNA-seq renews the role of the microvasculature in human atherosclerosis

  Atherosclerosis is a pervasive contributor to ischemic heart disease and stroke. Despite the advance of lipid lowering-therapies and antihypertensive agents, the residual risk of an atherosclerotic event remains high and developing therapeutic strategies has proven challenging. This is due to the complexity of atherosclerosis with a spatial interplay of multiple cell types within the vascular wall. Here we generate an integrative high-resolution map of human atherosclerotic plaques combining single-cell RNA-seq from multiple studies and spatial transcriptomics data from 12 human specimens, with different stages of atherosclerosis. We show cell-type and atherosclerosis-specific expression changes and spatially constrained alterations in cell-cell communication. We highlight the possible recruitment of lymphocytes via ACKR1 endothelial cells of the vasa vasorum, the migration of vascular smooth muscle cells towards the lumen by transforming into fibromyocytes, and cell-cell communication in the plaque region, indicating an intricate cellular interplay within the adventitia and the subendothelial space in human atherosclerosis.

  Dataset EGAD50000000936

• Sequencing_probands_and_families_with_severe_insulin_resistance_syndromes

  This is an ongoing project and continuation to all the sequencing we have been doing over the last few years. We have some additional families and probands with syndromes of insulin resistance not previously sequenced within uk10k or other core funded projects. We would like to complete the sequencing in all of the good quality families and probands we have, this would require another ~50 samples to be WES sequenced. This cohort has already proven to be a rich source of interesting findings with papers in Science and Nature genetics.

  Study EGAS00001000488

• Genomic analysis of HPV positive versus HPV negative esophageal adenocarcinoma

  High-risk human papillomavirus (hr-HPV) has been implicated in a subset of patients with esophageal adenocarcinoma (EAC). We therefore hypothesized that HPV associated EAC may have distinct genomic aberrations compared with viral negative esophageal cancer as shown in Head and Neck cancer and cervical cancer. Whole exome sequencing (WES) was performed to explore the mutational landscape and potential molecular signature of HPV positive versus HPV negative EAC, which includes four hr-HPV-positive and 8 HPV-negative treatment naive fresh-frozen EAC tissue specimens and matched normal tissues.

  Study EGAS00001001340

• Mesothelioma Genomics Study - WGS tumour/normal pairs

  Malignant mesothelioma (MM) is an incurable and aggressive tumour that occurs principally in the pleura as a consequence of inhaling asbestos fibres. There are >15,000 cases per annum worldwide, the incidence is increasing and Australia has one of the world's highest incidence rates. Surgery, chemotherapy and radiotherapy (or their combinations) all feature in the clinical management but do not impact significantly on overall survival. This study uses whole genome sequencing (WGS) with the aim of identifying mesothelioma-related genomic alterations and potentially identifying novel treatment strategies.

  Study EGAS00001002299

• ALPI deficiency and inflammatory bowel disease

  Inflammatory bowel diseases (IBDs) are complex and severe disorders ascribed to alterations in the dialogue between the microbiota and the host immune system (Bouma & Strober, 2003; Maloy & Powrie, 2011). By using whole‐exome sequencing (WES), we report the identification of compound heterozygous ALPI mutations in two unrelated patients displaying severe intestinal inflammation and autoimmunity. ALPI encodes the Intestinal alkaline phosphatase, a brush border metalloenzyme that catalyses phosphate hydrolysis of the lipid moiety of LPS and thereby drastically reduces LPS pro‐inflammatory activity (Schromm et al, 1998; Goldberg et al, 2008).

  Study EGAS00001002847