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• Zimbabwe Mendelian Disorders Genomics DAC

  Data Access Committee responsible for reviewing and approving access requests to human genomic data generated from individuals with suspected Mendelian disorders. The DAC ensures ethical use of genomic data in accordance with institutional, national, and international guidelines, protecting participant privacy while enabling responsible data sharing for research purposes.

  Dac EGAC50000000963

• Dataset for "HPV integration induces gene fusions" (pacBio)

  pacBio whole-genome sequencing data for "HPV integration induces gene fusions" We performed long read whole-genome sequencing on four HPV+ head and neck cancer samples using pacBio HiFi. The sequence reads were submitted in fastq format.

  Dataset EGAD50000001304

• Dataset for WGS and RNA melanoma samples

  This dataset contains WGS and RNA sequencing data for 4 melanoma samples. Sequencing was performed on Illumina Novaseq 6000 and Illumina HiSeq X. The sequencing was always paired.

  Dataset EGAD50000000093

• Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS)

  Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS). The dataset includes 21 samples from 7 families with BAMS; see Gordon et al, Nature Genetics, 2017.

  Dataset EGAD00001003130

• Whole exome sequencing of human and mouse sarcoma samples for personalized therapy

  Whole exome sequencing of human and mouse sarcoma samples for creation of personalized therapy options. Tissues were sequenced directly; no interventions or alterations were made to the tissue samples

  Dataset EGAD00001004885

• Exome sequencing of Non-syndromic Congenital Heart Defects (2019-04-24)

  Exome sequencing of ~1,800 patients with non-syndromic Congenical Heart Defects (CHD) to identify genes enriched for damaging rare variants that increase risk of CHD . This dataset contains all the data available for this study on 2019-04-24.

  Dataset EGAD00001004975

• Data for the genome‐wide association study of cutaneous leishmaniasis in Brazil

  DNAs were genotyped on Illumina Infinium HumanCoreExome Beadchips (Illumina Inc., San Diego, CA, USA) with probes for 551,004 single nucleotide variants (SNVs): 282,373 informative across ancestries; 268,631 exome-focused. Human genome build 37 (hg19) was used.

  Dataset EGAD00001006681

• Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing

  This dataset includes raw nanopore, base-called, and 6mA frequency data for EcoGII-treated NA12878 and MCF7 chromatin samples. It also includes raw nanopore data for the HG002 EcoGII-treated DNA.

  Dataset EGAD00001015374

• Thymic epithelial transplantation for complete DiGeorge syndrome Spatial (2026-01-19)

  Spatial transcriptome analysis of thymic cells from children with syndromic diseases such as Trisomy 21 and inflammatory/autoimmune diseases such as myasthenia gravis. . This dataset contains all the data available for this study on 2026-01-19.

  Dataset EGAD00001015798

• comparing the snRNA-seq from placentas of mothers with or without obesity

  Obesity poses risks to maternal health and increases the likelihood of short- and long-term adverse pregnancy outcomes in the offspring. The placenta, a key organ at the maternal-fetal interface, responds to maternal obesity and regulates fetal growth. To investigate the molecular features of physiological adaptation, we perform single-nuclei RNA-seq on human placentas and compared the transcriptomic profiles of women with obesity delivering appropriate- or large-for-gestational age (i.e., AGA and LGA) babies with those from normal-weight healthy controls with AGA babies. The snRNA-seq libraries were generated with Chromium Single Cell 3’ kit v3.1 (10X Genomics) and sequenced on Illumina NovaSeq 6000 at Novogene.

  Study EGAS50000000834

• NIH Human Microbiome Project - Core Microbiome Sampling Protocol A (HMP-A)

  This first clinical study of the Human Microbiome Project (HMP) addresses whether individuals share a core human microbiome. It involves broad determination of the microbiota found in five anatomical sites: the oral cavity, skin, nasal cavity, gastrointestinal tract and vagina. This study will enroll approximately 300 healthy male and female adults, 18-40 years old, from two geographic regions of the US: Houston, TX and St. Louis, MO. The participation of healthy individuals will create a baseline for discovery of the core microbiota typically found in various areas of the human body. The information from this initial study can then be used to help assess the changes in the complement of microbiota found on or within diseased individuals.

  Study phs000228

• A Large-Scale, Consortium-Based Genomewide Association Study of Asthma

  We carried out a genomewide association study by genotyping 10,365 persons with physician-diagnosed asthma and 16,110 unaffected persons, all of whom were matched for ancestry. We used random-effects pooled analysis to test for association in the overall study population and in subgroups of subjects with childhood-onset asthma (defined as asthma developing before 16 years of age), later-onset asthma, severe asthma, and occupational asthma.

  Study EGAS00000000077

• Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001227

• Whole genome shotgun sequencing assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  Whole genome shotgun sequencing assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001228

• ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001229

• ChIP-Seq (H3K27me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K27me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001230

• ChIP-Seq (H3K36me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K36me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001231

• ChIP-Seq (H3K4me1) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K4me1) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001232

• ChIP-Seq (H3K4me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K4me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001233

• ChIP-Seq (H3K9me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K9me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001234

• ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001235

• E5103 Correlative Studies

  ECOG-ACRIN E5103 (E5103) was a phase III adjuvant breast cancer trial that randomized 4994 patients with node-positive or high-risk node-negative breast cancer to intravenous doxorubicin and cyclophosphamide every 2 or 3 weeks (at the discretion of treating physician), for four cycles of adriamycin and cyclophosphamide (AC) followed by 12 weeks of weekly paclitaxel (80 mg/m2) alone (Arm A), or to the same chemotherapy with either concurrent bevacizumab (Arm B), or concurrent plus sequential bevacizumab (Arm C). To develop predictive genetic biomarkers for chemotherapy efficacy and toxicities, we have successfully performed genome-wide genotyping and whole exome sequencing in the germline (blood) DNA of 3215 and 672 patients, respectively, from the E5103 trial to investigate the association of genetic variants with chemotherapy efficacy and toxicities. Case and control studies were performed with genome-wide analyses (GWAS) and whole exome analyses (WES) across all arms of E5103 to identify genotypes at single-nucleotide polymorphisms (SNPs) and deleterious gene mutations that were associated with paclitaxel-induced peripheral neuropathy (TIPN). Through GWAS, we have identified a SNP, rs3125923, and through WES, Cytochrome P450 oxidoreductase (POR), that was significantly associated with grade 3-4 TIPN.

  Study phs003201

• Single Nucleus Transcriptomes from the Ventral Midbrain of Opioid Overdose Cases and Controls

  We generated ventral midbrain single nuclei RNA-seq libraries for 95 brain donors, including 45 subjects with documented histories of opioid abuse and overdose, and 50 demographically-matched, opioid-free control subjects, collected from two geographically distinct regions within the U.S. (greater Detroit area, Michigan and Miami, Florida). Each sample included both substantia nigra and the adjacent ventral tegmental area. Nuclei were processed in pools of 3-4 brains using the 10X Chromium system followed by Illumina sequencing, read alignment and processing by 10X Cellranger.

  Study phs003260

• A Prospective Study of Lifestyle, the Gut Microbiome, and Diverticulitis

  By leveraging a large-scale collection of stool specimens (Micro-N) within the Nurses' Health Study II, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 case women with a diagnosis of diverticulitis requiring antibiotics or hospitalization, with each matched to a control woman without diverticulitis during the same time period accounting for age, race, and month of stool collection (total N=242). We found microbiome and metabolomic profiles differed in diverticulitis cases compared to controls. Data deposited include metagenomic sequencing data (after removing the human sequences) and metabolomics data.

  Study phs003531

• Single-cell RNA sequencing of control and Notch inhibitor treated HCC PDX model

  We generated single-cell RNA-seq data for anti-Notch2 (n=3), anti-JAG1 (n=1) and anti-gD (n=4) treated LIV78 tumors. NCR nude mice bearing similarly sized LIV78 tumors (volumes between 300-900mm3) were injected intravenously with 30mg/kg body weight of either anti-Notch2, anti-Jag1 or anti-gD control antibody 72hrs prior to tumor harvest and tumor cell isolation. Following the depletion of CD45+ and Ter119+ cells, the samples were processed for single-cell RNA-seq (scRNAseq) as described previously (Long et al., 2019) using the Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual. cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq 2500 (Illumina) following the manufacturer’s sequencing specification (10X Genomics) to produce the resulting FASTQ files.

  Dataset EGAD50000000738