Ontology highlight
ABSTRACT:
PROVIDER: PRJNA285925 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Texas Cancer Research Biobank Open Access Data Sharing: Exome Project
| PRJNA284596 | ENA
Project description:Texas Cancer Research Biobank Open Access Data Sharing: Genome Project
| PRJNA284598 | ENA
Project description:These samples are being analyzed by the Duke-UNC-Texas-EBI ENCODE consortium. Expression from these cell types will compared to three whole genome open chromatin methodologies: DNaseI hypersensitivity (DNase-seq), Formaldehyde-Assisted Isolation of Regulatory elements (FAIRE-seq), and Chromatin Immunoprecipitation (ChIP-seq) . For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2009-04-23 | GSE15805 | GEO
Project description:<p>AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) is an international pancancer registry of real-world data assembled through data sharing between 19 leading international cancer centers with the goal of improving clinical decision-making. The registry leverages ongoing clinical sequencing efforts (CLIA/ISO-certified) at participating cancer centers by pooling their data to create a novel, open-access registry to serve as an evidence base for the entire cancer community. Genomic and baseline clinical data from more than 70,000 tumors is accessible through the efforts of our strategic and technical partners, Sage Bionetworks and cBioPortal. The consortium and its activities are driven by openness, transparency, and inclusion to ensure that the project output remains accessible to the global cancer research community and ultimately benefits patients.</p>
| phs001337 | dbGaP
Project description:We generated novel genomic resources by mapping regions of open-chromatin, indicators of cis-regulatory activity, in immortalized corneal epithelial and stromal cell lines, using the assay for transposase accessible chromatin followed by sequencing (ATAC-seq). Overlaying these data with the well-powered UK Biobank CRF-GWAS study demonstrates the keratocyte cells to be a suitable system to guide future functional characterisation of, at least some, regulatory networks modulated by CRF-associated variants.
2020-12-01 | GSE150064 | GEO
Project description:<p>The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), which are both part of the National Institutes of Health, U.S. Department of Health and Human Services.</p> <p>TCGA projects are organized by cancer type or subtype. Click <a href="http://cancergenome.nih.gov/cancersselected" target="_blank">here</a> for a current list of cancer types selected for study in TCGA.</p> <p>Data from TCGA (e.g., gene expression, copy number variation and clinical information), are available via the <a href="https://gdc.cancer.gov/" target="_blank">Genomic Data Commons (GDC)</a>.</p> <p>Data from TCGA projects are organized into two tiers: <b>Open Access and Controlled Access</b>. <ul> <li>Open Access data tier contains data that cannot be attributed to an individual research participant. The Open Access data tier does not require user certification. Data in Open Access tier are available in the TCGA Data Portal.</li> <li>Controlled Access data tier contains individual-level genotype data that are unique to an individual. Access to data in the Controlled Access data tier requires user certification through <a href="https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?login=&page=login" target="_blank">dbGaP Authorized Access</a>.</li> <li>Controlled Access data types consist of the following: <ul> <li>Individual germline variant data (SNP .cel files)</li> <li>Primary sequence data (.bam files), which are available at GDC</li> <li>Clinical free text fields</li> <li>Exon Array files (for Glioblastoma and Ovarian projects only)</li> </ul> </li> </ul> </p> <p><b>NOTE: TCGA strives to release most data in the open access tier. Individual genotype or sequence files are prominent exceptions. Commonly requested files such as descriptions of somatic mutations or clinical data are open access.</b></p> <p>Please go to this page: <a href="https://tcga-data.nci.nih.gov/docs/publications/" target="_blank">https://tcga-data.nci.nih.gov/docs/publications/</a> to access all data associated with TCGA tumor specific publications.</p> <p><b>The TCGA study is utilized in the following dbGaP substudies.</b> To view genotypes and other molecular data collected in these substudies, please click on the following substudies below or in the "Substudies" section of this top-level study page phs000178 TCGA study. <ul> <li><a href="./study.cgi?study_id=phs000854">phs000854</a> Genome-wide Analysis of Noncoding Regulatory Mutations in Cancer</li> </ul> </p>
| phs000178 | dbGaP
Project description:Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. For a quantitative getic analysis of chromatin regulation, we generated open chromatin maps of 100 yeast samples including the parental strains (BY and RM, and two replicates for each) and their descendants by using the FAIRE-seq technique Open chromatin in two parental strains and 94 segregants of their crossing
2012-11-02 | E-GEOD-33466 | biostudies-arrayexpress
Project description:A patient-derived epithelium-only colon rectal organoid, also referred to as a colonoid, was generated from an adenoma (associated with a resection surgery of an invasive moderately differentiated colorectal adenocarcinoma) as part of the development of an on-going organoid biobank at the Michigan Medicine Translational Tissue Modeling Laboratory (TTML, www.UmichTTML.org). The genomic variant signature of this adenoma colonoid was characterized using whole exome sequencing in order to access genomic concordance between the source patient tissue (adenoma and histologically normal tissue 10 cm from lesion) and the in vitro culture, as well as to access genomic stability of the culture over time at 2 and 6.5 months in culture.
2020-12-22 | E-MTAB-9936 | biostudies-arrayexpress