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• MASS_Pilot: Muscle and Ageing Science Study - Collaboration with Wellcome Sanger Institute to characterise skeletal muscle ageing using Human Cell Atlas approaches (2025-07-31)

  Transcriptomic analysis of skeletal muscle, to understand the mechanisms of muscle ageing. . This dataset contains all the data available for this study on 2025-07-31.

  Dataset EGAD00001015670

• WGS dataset of Hepatoblastoma tumoroid biobank as a key resource for tumour genetics

  WGS dataset of Hepatoblastoma tumoroid biobank with WGS of tumor and matched tumoroids

  Dataset EGAD00001015671

• Additional RNAseq data of metastatic breast cancer samples

  Paired-end RNA sequencing data from 33 metastatic breast cancer samples. Sequencing was performed on the Illumina NovSeq 6000 using NEBNext Single Cell and Low Input RNA Library Prep Kit for Illumina.

  Dataset EGAD00001015678

• Genomic and transcriptomic determinants of host susceptibility, protection, and viral mutation in experimental SARS CoV-2 infection: RNA (2025-08-11)

  Single-cell profiling of healthy adult volunteers that were inoculated with SARS-CoV-2. . This dataset contains all the data available for this study on 2025-08-11.

  Dataset EGAD00001015679

• Dataset for ARHGAP11A knockout and control organoid cells.

  This dataset contains 9 RNA sequencing samples of hiPSC-derived forebrain organoid ARHGAP11A knockout and hiPSC-derived forebrain organoid control cells. Sequencing was performed on Illumina NovaSeq 6000. The sequencing was always paired.

  Dataset EGAD00001015706

• A study of the immune system in patients with peripheral inflammatory neuropathy (CIDP): RNA adult (2025-10-02)

  Leveraging single-cell sequencing technologies to shed light on the immune aetiology of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) . This dataset contains all the data available for this study on 2025-10-02.

  Dataset EGAD00001015725

• Dataset for ChIP and Transcriptomic sequencing of neuroblastoma tumor samples(hipo)

  This dataset contains ChIP and Transcriptomic sequencing of 32cneuroblastoma tumor samples. The sequencing was performed on Illumina HiSeq 2000 and Illumina HiSeq 4000 respectively.

  Dataset EGAD00001015808

• Immune Profiling in Patients with High-Risk Smoldering Myeloma

  Single-cell RNA-sequencing identifies immune biomarkers of response to immunotherapy in patients with high-risk Smoldering Multiple Myeloma (SMM). We conducted a Phase II trial of the immunotherapeutic anti-SLAMF7 antibody, Elotuzumab, in combination with Lenalidomide and Dexamethasone (E-PRISM study), to determine the utility and safety of early immunotherapy in patients with high-risk SMM and develop biomarkers for optimal patient selection and monitoring of response to treatment.There is an overlap in subjects between this study and dbGaP accession phs001323.

  Study phs002476

• Bladder Chemotherapy Responders

  Cisplatin-based chemotherapy is the standard of care for patients with muscle invasive urothelial carcinoma. Pathologic downstaging to pT0/pTis after neoadjuvant cisplatin-based chemotherapy is associated with improved survival, and some patients with metastatic disease achieve complete responses to these therapies. However, the molecular determinants of cisplatin response are incompletely understood. We performed whole exome sequencing on tumor and germline DNA from patients with muscle invasive or metastatic urothelial carcinoma who received cisplatin-based chemotherapy to identify somatic mutations that occurred preferentially in cisplatin responders.

  Study phs000771

• Comprehensive Analysis of Structural Variants in Breast Cancer Genomes Using Single Molecule Sequencing

  This study used the SKBR3 breast cell line and tumor/normal organoids derived from breast tissue to explore the utility of long read sequencing for detecting structural variants in complex samples. Three technologies were used to characterize the samples: Illumina/10X, Pacific Biosciences, and Oxford Nanopore. Methylation results were derived from the Oxford Nanopore data. It is hoped that this resource will better help researchers better understand the utility of long read sequencing in cancer samples.

  Study phs002210

• The Nephrotic Syndrome Study Network (NEPTUNE)

  The Nephrotic Syndrome Study Network (NEPTUNE) is a collaborative investigational infrastructure of 40 North American sites for conducting clinical and translational research in Focal Segmental Glomerulosclerosis (FSGS), Membranous Nephropathy (MN), and Minimal Change Disease (MCD). NEPTUNE provides prospective, un-blinded, standardized evaluation of clinical and molecular outcomes in two cohorts: A) adults and children with incident or prevalent, biopsy-proven FSGS, MN, or MCD, recruited at the time of first biopsy, and B) children with incident Nephrotic Syndrome without a diagnostic kidney biopsy.

  Study phs003210

• Genome Wide Association Study of Chronic TMD: Discovery Phase

  The OPPERA project is investigating effects of genetic, physiological, psychological and clinical factors on the risk of developing painful temporomandibular disorder (TMD). This case-control study is a discovery-phase genome wide association study that aims to identify commonly-occurring genetic variants associated with chronic TMD. It represents the first step in a series of studies that seek to identify the genetic background of TMD. For related phenotype and targeted genotype data, please see additional studies from the OPPERA project at dbGaP phs000761).

  Study phs000796

• GUARDIAN: The Insulin Resistance Atherosclerosis Family Study (IRASFS)

  TThe IRAS Family Study was a family study designed to examine the genetic and epidemiologic basis of glucose homeostasis traits and abdominal adiposity. Briefly, self-reported Mexican pedigrees were recruited in San Antonio, TX and San Luis Valley, CO. Probands with large families were recruited from the initial non-family-based IRAS Study, which was modestly enriched for impaired glucose tolerance and T2D. GUARDIAN includes 1,024 individuals in 88 pedigrees from the IRAS Family Study. Insulin sensitivity was obtained by FSIGT.

  Study phs001008

• Characterization of Neoantigen-reactive T cells by Single-Cell Analysis

  Through CITE-seq and TCR-seq analysis of non-small cell lung cancer (NSCLC) tumor-infiltrating lymphocytes (TIL), we developed a neoantigen-reactive T-cell signature based on clonotype frequency and CD39 protein and CXCL13 mRNA expression. There are four datasets from four NSCLC cases. Each dataset includes (1) Transcriptome of tumor infiltrating lymphocytes (TIL), (2) Cell surface protein expression on TIL by Feature barcoding, (3) T-cell receptor analysis of TIL, and (4) Reference file for feature-barcoding antibodies.

  Study phs002792

• A Phenotypic and Genomics Approach in a Multi-Ethnic Cohort to Subtype Systemic Lupus Erythematosus

  Systemic lupus erythematosus (SLE) is a complex autoimmune disease that affects multiple organ systems and varies in severity across different populations. To examine the clinical heterogeneity of SLE, we sought to identify different lupus subtypes within our multi-ethnic cohort using a clustering approach. Additionally, with genome-wide methylation and genotype data generated for our cohort, we applied integrative methods to investigate genetic and epigenetic risk factors. This integrative and computational approach revealed molecular differences associated with phenotypic clusters.

  Study phs001850

• NHLBI TOPMed: Children's Health Study (CHS) Integrative Genomics and Environmental Research of Asthma (IGERA)

  The Integrative Genomics and Environmental Research of Asthma (IGERA) Study was proposed to collect immortalized cell lines, RNA, cDNA and DNA from 400 well-characterized subjects who participated in the southern California Children's Health Study (CHS) and to develop an accompanying database for these samples consisting of extensive phenotype, exposure, genome-wide genotype, gene expression, and methylation data. A subset of Hispanic-White participants (n=160) were included in the TOPMed project, including 77 asthma cases and 83 controls.

  Study phs001603

• Breast Cancer Genome Guided Therapy Study (BEAUTY)

  The Breast Cancer Genome Guided Therapy Study (BEAUTY) is a prospective neoadjuvant clinical study enrolling 140 women with Stage I-III breast cancer. The goals of this study were to 1) perform comprehensive sequencing of germline and tumor tissues (exome and RNA seq), 2) identify genomic alterations and perturbed pathways associated with response/resistance to standard chemotherapy, and 3) develop patient-derived xenograft (PDX) for testing of therapeutic regimens chosen on the basis of alterations identified by genetic sequencing.

  Study phs001050

• Myocardial Infarction Genetics Exome Sequencing Consortium: BioImage Study

  The BioImage Study (BioImage Study: A Clinical Study of Burden of Atherosclerotic Disease in an At-Risk Population, NCT00738725), is a prospective, observational study aimed at characterizing subclinical atherosclerosis in U.S. adults (55 to 80 years old) at risk for clinical atherosclerotic cardiovascular disease (PMID: 25790876). All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Illumina's ICE Capture reagent and sequencing was performed on an Illumina HiSeq 2000 or 2500.

  Study phs001058

• Decade-Long Leukemia Remissions with Persistence of CD4+ CAR T-Cells

  Two patients with chronic lymphocytic leukemia (CLL) were treated with CD19 targeted CAR T therapy and followed over several years. Peripheral blood from both patients at multiple time points was collected, and 5' CITE-Seq with TCR profiling was performed on sorted CD3+CAR+ T cells at multiple time points. Here, we deposit the raw sequencing data for these single-cell experiments. Processed and de-identified data (e.g. cellranger output, Seurat objects) have been made available on a separate public data repository.

  Study phs002931

• Genome-Wide Analysis of Aberrant Position and Sequence of Plasma DNA Fragment Ends in Patients With Cancer

  This study investigated fragmentation characteristics in plasma cell-free DNA and evaluated the relevance of such analysis for cancer diagnostics. Specifically, we performed whole genome sequencing (WGS) of healthy individuals and cancer patients, and evaluated genome-wide coverage and sequences surrounding fragment ends. This was a retrospective study of archived plasma samples. The WGS data are available through this submission. Detailed study design and findings were published in Budhraja et al. Science Translational Medicine 2023.

  Study phs003170

• A Pilot Study to Evaluate Tissue- and Plasma-based DNA Driver Mutations in a Cohort of Patients with Pancreatic Intraductal Papillary Mucinous Neoplasms

  This is a retrospective study aimed at evaluating concordance between intraductal papillary mucinous neoplasm (IPMN) tissue and patient-matched plasma circulating tumor DNA (ctDNA) using a targeted sequencing approach. Archival solid tissue genomic DNA was available for 46 patient FFPE blocks patient-matched plasma ctDNA was available from 15 of those patients. All tissues were obtained pre-treatment from patients with an IPMN diagnosis and subjected to Qiagen custom next generation sequencing panel.

  Study phs003043

• Germline genome-wide association studies in women receiving neoadjuvant chemotherapy with or without bevacizumab on NSABP B-40

  Neoadjuvant chemotherapy (NAC) for breast cancer is widely employed. We performed genome-wide association studies (GWAS) to determine if germline genetic variability was associated with benefits, in terms of pathological complete response (pCR), disease-free survival (DFS), and overall survival (OS), in patients entered on the NSABP B-40 NAC (National Surgical Adjuvant Breast and Bowel Project, B-40, Neoadjuvant Chemotherapy) trial where some patients were randomized to receive bevacizumab, in addition to chemotherapy.

  Study phs001365

• Therapeutic Genetics and Disease Modeling in LAMA2-CMD

  Merosin-deficient congenital muscular dystrophy (MDC1A) is an autosomal recessive disorder caused by mutations in the LAMA2 gene, resulting in a defective form of the extracellular matrix protein laminin-α2 (LAMA2). Individuals diagnosed with MDC1A exhibit progressive muscle wasting and declining neuromuscular functions. No treatments for this disorder are currently available. This study involves transcriptomic comparison analysis between MDC1A patient fibroblasts and healthy control fibroblasts to reveal changes in gene expression that contribute to LAMA2 congenital muscular dystrophy (LAMA2-CMD).

  Study phs003250

• High-Throughput and High-Dimensional Single Cell Analysis of Antigen-Specific CD8+ T Cells

  We developed a high-dimensional, tetramer associated T cell receptor sequencing (TetTCR-SeqHD) method to simultaneously profile cognate antigen specificities, TCR sequences, targeted gene-expression, and surface protein expression. Cultured antigen-specific CD8+ T cell clones were studied as a proof-of-concept experiment. In addition, both the antigen specific CD8+ T cells from healthy subjects and Type I diabetic patients were investigated. 18 individually consented subjects pooled into four groups for sample processing

  Study phs002441

• Single-Cell Genome Sequencing of Gastrointestinal Carcinomas

  We experimentally derived copy number profiles and transcriptome profiles of gastrointestinal cancers using single cell sequencing. Using a microfluidic droplet partitioning system, we isolated individual cells of a suspension from a primary solid tumor into droplets. These droplets tag the resultant genomic or transcriptomic material with an identifying barcode that enables bioinformatic single cell tracking. From this joint analysis, we determined the overall level of genomic instability for gastrointestinal cancers as well as transcriptomic consequences from these events.

  Study phs001711