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• small RNA-sequencing and RNA-sequencing of human brain tissue with temporal lobe epilepsy

  This data set contains the raw .fastq files from two RNA-sequencing experiments and two small RNA-sequencing experiments. Both control brain tissue and tissue from sufferers of mesial temporal lobe epilepsy were sequenced. Two different brain regions were sequenced; the cortex and the hippocampus. For more details please see: Mills, James D., et al. "Coding and non-coding transcriptome of mesial temporal lobe epilepsy: Critical role of small non-coding RNAs." Neurobiology of disease 134 (2020): 104612.

  Dataset EGAD00001005735

• TK-EPN862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - RNAseq

  In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. RNAseq data (paired end) provided here correspond to Primary tumour, two metastatic lesions (one spinal, one cranial), and a patient-derived xenograft derived from the patient.

  Dataset EGAD00001009870

• RNA-seq analysis of CCO+/CCO- hepatocytes in normal human liver

  RNAseq data from Passman et al 2023. Clonal CCO-deficient hepatocyte patches and nearby CCO-proficient hepatocytes were identified in morphologically normal human livers and sampled at varying distances along the PT-CV axis. Samples are characterised according to their location within the liver lobule, with "PT" denoting samples abutting the portal triad, "CV" denoting samples abutting the central hepatic vein, and "Mid" sampled acquired midway between these structures. Analysis was performed on an Illumina Nextseq using a high output kit and 100 single-end cycles.

  Dataset EGAD00001010033

• International Collaboration of Incident HIV and HCV in Injecting Cohorts (InC3)

  This study represents a merged international multi-cohort project of pooled biological and behavioral data from ten prospective cohorts of injection drug users (Grebely J, Morris MD, Rice TM, Bruneau J, Cox AL, Kim AY, et al., 2012, PMID: 23203695). Of the 10 cohorts, six provided data and samples for the genome wide association study (GWAS) entitled “Genetic Analysis of Opioid Addiction in People Who Inject Drugs”. The InC3 cohorts included in the GWAS were: i) Australian Trial in Acute Hepatitis C (ATAHC-I, Sydney); ii) Hepatitis C Incidence and Transmission Study in Prison (HITS-p) (Sydney); iii) Hepatitis C Incidence and Transmission Study in Community (HITS-c) (Sydney); iv) HepCo Study (Montreal); v) SuperMIX Study (combining the Networks II & MIX studies, Melbourne); and vi) the UFO Study (San Francisco).

  Study phs002310

• African American Breast Cancer GWAS

  The GWAS includes African American participants from 9 epidemiological studies of breast cancer, comprising a total of 3,153 cases and 2,831 controls (cases/controls: The Multiethnic Cohort Study (MEC), 734/1,003; The Los Angeles component of The Women's Contraceptive and Reproductive Experiences (CARE) Study, 380/224; The Women's Circle of Health Study (WCHS), 272/240; The San Francisco Bay Area Breast Cancer Study (SFBCS), 172/231; The Northern California Breast Cancer Family Registry (NC-BCFR), 440/53;The Carolina Breast Cancer Study (CBCS), 656/608; The Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort, 64/133; The Nashville Breast Health Study (NBHS), 310/186; and, The Wake Forest University Breast Cancer Study (WFBC), 125/153). Quality control of the GWAS data and additional details can be found in Chen et al. Hum Genet. 2013 (PMID: 22923054)

  Study phs000851

• A Single Cell Atlas of MMRd and MMRp Colorectal Cancer

  Immune responses to cancer vary across cancer types and patients. Colorectal cancer tumors with mismatch repair-deficiency (MMRd) show an elevated immune cell activity as compared to mismatch repair proficient (MMRp) tumors. To understand the immune response patterns in these two types of colorectal cancer, we transcriptionally profiled 371,223 tumor and adjacent normal cells from 28 MMRp and 34 MMRd patients. Unsupervised analysis identified 88 cell subsets, from 7 distinct cell clusters (that contain epithelial, malignant, stromal and immune cell lineages), and an associated compendium of 204 gene expression programs. Examination of these cell subsets and programs revealed extensive transcriptional and spatial remodeling of malignant, stromal and immune cells in MMRd and MMRp tumors. This dataset was generated as part of a published study (Pelka, Hofree, Chen, et al., Cell 2021 Sep 2;184(18):4734-4752; PMID: 34450029).

  Study phs002407

• HCI-PDX Trial Center for Breast Cancer Therapy

  The HCI-PDX Trial Center for Breast Cancer Therapy study is a collection of patient-tumor samples that are serially established as patient-derived tumor xenografts (human tumor in mouse) and matching organoids. For this study, we describe valuable methods and resources to generate organoids and use them as cost-effective models for precision drug screens. This study leveraged whole-exome sequencing, RNAseq, and SNP-array data to illustrate how the heterogeneity of tumors is preserved in xenograft and organoid models. Sequencing files are provided for whole-exome and RNAseq data. Processed copy number variant calls from the SNP arrays are also available. A full description of the study can be found in the article entitled, "A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology," written by Guillen et al., 2022 in Nature Cancer (PMID: 35221336).

  Study phs002479

• Beta-Blocker Evaluation in Survival Trial (BEST-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives The Beta-Blocker Evaluation of Survival Trial was designed to determine whether bucindolol hydrochloride- a nonselective beta-adrenergic blocker and mild vasodilator- would reduce the rate of death from any cause among patients with advanced heart failure and to assess its effects in various subgroups defined by ethnic background and demographic criteria- specifically women and members of minority groups. Background Although beta-adrenergic-receptor antagonists reduce morbidity and Mortality in participants with mild-to-moderate chronic heart failure, their effort on survival in participants with more advanced heart failure is unknown. Participants There were 2,708 participants. Conclusions Bucindolol resulted in no significant overall survival benefit. (Krause-Steinrauf et al., 2001, PMID: 11386264).

  Study phs003730

• APOL1 Risk Variants Induce Metabolic Reprogramming of Podocytes in Patient-Derived Kidney Organoids

  Apolipoprotein L1 (APOL1) high-risk genotypes G1 and G2 are responsible for the increased risk of chronic kidney disease (CKD) in the African-American population, especially in the presence of interferon gamma (IFN-γ). Here, we applied single cell transcriptomics on kidney organoids generated from patient-derived induced pluripotent stem cells (iPSCs) to model human APOL1 nephropathy. iPSCs were generated from fibroblasts of two patients with APOL1 nephropathy homozygous for G1 or G2 risk variants, and an isogenic control (G0) was created by gene correction. Kidney organoids were generated according to previously published protocol (Takasato M et al. Nat. Protoc. 2016) and treated with IFN-γ for two days to induce APOL1. Twenty-four hours after IFN-γ removal, treated organoids from all three lines that were cultured in parallel were harvested for single cell transcriptomics.

  Study EGAS50000001223

• Colorectal advanced adenomas NKI-AvL TGO COCOS series

  Colorectal cancer (CRC) develops from normal epithelium, through a benign precursor lesion called adenoma, by accumulation of genetic alterations affecting oncogenes and tumour suppressor genes. About 5% of colorectal adenomas are estimated to progress to CRC. However, it is important to identify which adenomas actually carry a high-risk of progression, because these serve as intermediate endpoints for e.g. screening programs. In clinical practice, adenomas with a size of ≥10 mm, villous component and/or high-grade dysplasia, called advanced adenomas, are considered high-risk, although solid evidence for this classification is lacking. Specific DNA copy number changes are associated with adenoma-to-carcinoma progression.For this tissue dataset, we applied low-pass whole genome sequencing to 96 advanced adenomas. Advanced adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Study EGAS00001002952