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• Luminal Androgen Receptor-Enriched Triple Negative Breast Cancer

  This is a study to determine the efficacy of androgen receptor (AR) inhibitors in LAR (luminal androgen receptor)-enriched triple-negative breast cancer (TNBC) in the neoadjuvant setting. Twenty-four patients were treated with neoadjuvant AR inhibitor enzalutamide and paclitaxel for 12 weeks. Whole exome sequencing and RNA-sequencing was performed prior to treatment. The data for only two patients are consented for release through dbGaP. The remaining data are available under a Materials Transfer Agreement with the University of Texas MD Anderson Cancer Center.

  Study phs003586

• Single-cell and spatial atlas of steatotic liver disease-related hepatocellular carcinoma

  This study consists of the spatial transcriptomics data generated by : 1. Visium CytAssist Spatial Gene Expression for FFPE (10x) for steatotic liver disease-associated hepatocellular carcinoma (SLD-HCC) (n=7) and non-SLD-HCC (n=5) 2. CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex); NanoString, USA for n=4 SLD-HCC and n=4 non-SLD-HCC. The goal of this data is to compare SLD-HCC vs non-SLD-HCC as well as response to immunotherapy

  Study EGAS50000001034

• Activation-Induced Marker (AIM) Sequencing of Healthy Human T Cells

  T cells from five healthy human donors were stimulated with a peptide pool (CEFX, JPT) and anti-CD28/CD49d co-stimulation. Cells were then sorted based on activation (OX40 and PD-L1 for CD4s, CD137 for CD8s) and labeled with corresponding hashing antibodies prior to sequencing. In total, this dataset encompasses 42,370 cells (12,743 activation-induced marker (AIM)-positive, 15,369 AIM-negative, 14,258 Mock) for CITE-sequencing and TCR-sequencing of sorted activated, unactivated, and mock T cells derived from blood.

  Study phs004043

• Observational studies using advanced analytical techniques to understand the biological functions of kidney component cells

  The purpose of this study is to establish a foundation for understanding the functions of kidney component cells and the biology of renal disease. Single cell and spatial transcriptome analyses of human kidney component cells will be performed to analyze the gene expression profiles of those cells and explore their relationship between the gene expression profiles and clinical parameters. The research foundation established here is worthwhile for understanding disease mechanisms in the kidney or discovering novel therapeutic drugs for renal disease.

  Study JGAS000736

• Hip OA Functional Genomics

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of hip osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

  Study EGAS00001002483

• Knee_OA_Functional_Genomics

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of knee osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

  Study EGAS00001001899

• scEC&T-seq manuscript data

  This dataset includes all data produced in the study describing "scEC&T-seq", a method for parallel sequencing of extrachromosomal circular DNA and transcriptome in single cells. This dataset includes: - Illumina scEC&T-seq Circle-seq data (scCircle-seq) for a total of 626 single cells / nuclei - bam files - Illumina scEC&T-seq RNA-seq data (scRNA-seq-Illumina) for the same single cells / nuclei - bam files - Nanopore scCircle-seq data for 18 single cells - bam files - Nanopore bulk WGS for 2 cell lines and 2 primary tumor samples - bam files - Illumina bulk WGS for 2 cell lines - bam files - Illumina bulk Circle-seq data from 1 cell line - bam file - Illumina ChIP-seq H3K27me3 data from 1 cell line - fasta files + peaks bed file + coverage bw file

  Dataset EGAD00001010071

• Transdisciplinary Studies of Genetic Variation in Colorectal Cancer(CORECT): Axiom GWAS

  This study is part 1 of 2 for Schumacher et al, Nat Commun. 2015 Jul 7;6:7138. Part 1 is the original GWAS data for 9,259 participants on the Affymetrix Axiom platform of the studies listed below in the Inclusion Criteria.

  Study phs001856

• A Genomic Approach to Improved Diagnosis and Treatment of Neuroendocrine Tumors

  These are RNA-Seq samples from patients undergoing surgery for small bowel and pancreatic neuroendocrine tumors. Normal tissue, primary tumors, lymph nodes, and liver metastases were collected at surgery and stored in RNAlater until RNA extraction was carried out for RNA-Seq.

  Study phs001772

• Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

  Human intestinal organoids co-cultured with pro-inflammatory (M1) or anti-inflammatory (M2) human macrophages for 48 hours. 3 days after the co-culture alive cells were sorted and processed for single cell RNA sequencing

  Study EGAS50000000467

• RNA004 Nanopore DRS of peripheral blood

  Direct RNA Sequencing offers the capability of standard transcriptomic analyses + RNA modification analysis, which holds promising applications for future clinical workflows. To this end, we tested the newly available RNA004 kit on human peripheral blood and provide orthogonal GLORI measurement for benchmarking of m6A-detection.

  Study EGAS50000001201

• Comprehensive analysis of the abnormality of the genes in juvenile myelomonocytic leukemia

  To develop a simple and robust methylation test for risk stratification of patients with juvenile myelomonocytic leukemia. We used the DREAM method, a method for whole genome methylation analysis using NGS, to analyze methylation profiling of patients with juvenile myelomonocytic leukemia.

  Study JGAS000292

• Single-nucleus transcriptome sequencing of the ALS-FTD motor cortex after sorting by TDP-43

  Single-nucleus RNA-sequencing of NeuN+ nuclei of the post-mortem human primary motor cortex from patients with ALS-FTD confirmed for TDP-43 pathology, after sorting for TDP-43 signal, TDP-43 Low vs. TDP-43 High

  Study EGAS50000001566

• ATAC-seq data in normal colon mucosa

  This dataset includes ATAC-seq data generated in normal colon mucosa obtained in four healthy volunteers during colonoscopy indicated for colorectal cancer screening. Subjects had no lesions in the colon. Also includes one frozen sw480 colon adenocarcinoma cell line sample for piloting the protocol

  Study EGAS00001005281

• Integrative and comparative genomic analyses identify clinically relevant groups of pulmonary carcinoids and unveil the supra-carcinoids

  Multi-omic data for lung neuroendocrine neoplasms, including the first multi-omic sequencing data for the understudied lung atypical carcinoids. The data includes Whole-exomes, whole-genomes, RNA-seq, and EPIC 850K methylation array data.

  Study EGAS00001003699

• Genome-wide association data on male-pattern baldness

  The study comprises 1000Genomes imputed data for 581 MPB cases and 416 male controls. Cases are selected for age<40 and Hamilton-Norwood grade V-VII. Control include 270 males >60 years no signs of AGA (Hamilton-Norwood grade I).

  Study EGAS00001001354

• Synthetic genotypes and phenotypes of 500.000 individuals

  The goal of our study is to establish a pipeline for creating synthetic genotype and phenotype data on a Biobank scale. Such data can be used for developing new methodologies of analysis of common and rare diseases without risking de-identifying the underlying samples.

  Study EGAS00001006552

• August 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  August 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001006383

• August 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  August 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001005335

• May 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  May 2019 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001005060

• Genetic determinants of monocyte splicing are enriched for disease susceptibility loci including for COVID-19

  These data correspond to samples used in the following papers: 1. GWAS and meta-analysis identifies 49 genetic variants underlying critical Covid-19 2. Genetic determinants of monocyte splicing are enriched for disease susceptibility loci including for COVID-19. 3. Identification of Genetic Determinants of Transcriptional Response to Metformin in Primary Human Monocytes. They are the raw RNA sequencing files as used in all downstream analysis.

  Dataset EGAD00001010176

• September 2016 data update (bam/fastq/vcf) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  September 2016 data update (bam/fastq/vcf) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001002724

• January 2018 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  January 2018 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003962

• June 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  June 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003414

• Fastq files used for searching for variants associated with endometriosis at 9p21 region

  We performed target re-sequencing for 1.29 Mb interval of chromosome 9 (chr9:21299764–22590271, hg19). NimbleGen SeqCap EZ choice system was used as a target enrichment method (Roche Diagnostics). A DNA probe set complementary to the target region was designed by NimbleDesign. The libraries were sequenced on the Illumina MiSeq platform with 2×150-bp paired-end module (Illumina). Fastq files for 48 Japanese patients with endometriosis are deposited.

  Dataset EGAD00001001942