RNA-seq from 53 human tissue samples from the Genotype-Tissue Expression (GTEx) Project
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina MiSeq, Illumina HiSeq 2000
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-MTAB-2919 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
The Genotype-Tissue Expression (GTEx) project.
Nature genetics 20130601 6
Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the sci ...[more]
Similar Datasets
Project description:The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs. The present dataset contains RNA-seq from human reference/non-diseased tissues (thus, we have excluded K-562 cell line that is a chronic myelogenous leukemia cell line) from the Genotype-Tissue Expression (GTEx) Project (http://www.gtexportal.org/home/).
2016-12-07 | E-MTAB-5214 | biostudies-arrayexpress
Project description:Genotype-Tissue Expression Project (GTEx)
| PRJNA158505 | ENA
Project description:Genotype-Tissue Expression (GTEx) Common Fund Project
| PRJNA75897 | ENA
Project description:<p><b>Lay Description</b></p> <p>The aim of the Genotype-Tissue Expression (GTEx) Project is to increase our understanding of how changes in our genes affect human health and disease with the ultimate goal of improving health care for future generations. GTEx will create a database that researchers can use to study how inherited changes in genes lead to common diseases.</p> <p>GTEx researchers are studying genes in different tissues obtained from many different people. The GTEx project also includes a study of the GTEx donor consent process - this study will help ensure that the consent process and other aspects of the project effectively address the concerns and expectations of participants in the study. GTEx is a pioneering project that uses state-of-the-art protocols for obtaining and storing a large range of organs and tissues, and for testing them in the lab. Until now, no project has analyzed genetic variation and expression in as many tissues from the same person in such a large population as planned for GTEx.</p> <p><b>Scientific Description</b></p> <p>Understanding the role of variation in the human genome is crucial to elucidating genetic contributions to human health and disease. Despite the results of genome-wide association studies (GWAS) documenting strong statistical associations between genetic variation and human traits, the functional role for most of these variants is largely unexplained. Nearly 90% of these GWAS-implicated sites lie outside of protein-coding sequences, suggesting that these variants might regulate gene expression.</p> <p>The goal of the Genotype-Tissue Expression (GTEx) project is to establish a resource database and tissue biobank in which to study the relationship between genetic variation and gene expression and other molecular phenotypes in reference/non-diseased tissues. The ultimate resource will include approximately 960 post-mortem donors with several dozen tissues from each, a resource large enough to study both <i>cis</i>- and <i>trans</i>- gene expression quantitative trait loci (eQTLs). Some tissue will also be banked for additional molecular analyses. To request biosamples, please see the <a href="http://www.gtexportal.org/home/samplesPage" target="_blank">Biobank page</a> for more information.</p> <p>GTEx was initially funded as a 2-year pilot project by the NIH Common Fund (CF) in 2010, and has been scaled up after demonstration of feasibility. The project will collect and analyze RNA levels in many different human tissues and each donor will be characterized for germline genetic variation through dense genotyping arrays and sequencing of either whole exomes or whole genomes.</p> <p>By treating RNA expression levels as quantitative traits, eQTLs will be identified as sites containing genetic variation that correlate with changes in RNA expression. Such eQTLs have been associated with 4%-12% of expressed human genes, and with common complex human diseases, including obesity, atherosclerosis, type 2 diabetes, Crohn's disease, and asthma. Additionally, few studies have examined the tissue specificity of eQTLs. A subset of banked tissue samples will also be analyzed for other molecular phenotypes, such as DNA methylation, DNaseI hypersensitivity sites, and proteomics. The GTEx project will thus serve as a resource database and tissue bank for many future studies, especially for understanding the functional basis of inherited susceptibility to disease.</p> <p>All GTEx releases since Version 5 follow the NIH Genomic Data Sharing (GDS) Policy whereby there are no restrictions on use or publication after release. Additional information about the GTEx Data Release and Publication policy can be found on the GTEx Data Portal at <a href="http://www.gtexportal.org" target="_blank">www.gtexportal.org</a>.</p>
| phs000424 | dbGaP
Project description:<p><b>Lay Description</b></p> <p>The aim of the Genotype-Tissue Expression (GTEx) Project is to increase our understanding of how changes in our genes affect human health and disease with the ultimate goal of improving health care for future generations. It was launched in 2010 as a two-year pilot project supported by the Office of the Director, National Institutes of Health (NIH). GTEx will create a database that researchers can use to study how inherited changes in genes lead to common diseases.</p> <p>GTEx researchers are studying genes in different tissues obtained from many different people. The GTEx project also includes a study to explore the effectiveness of the GTEx donor consent process - this study will help ensure that the consent process and other aspects of the project effectively address the concerns and expectations of participants in the study. GTEx is a pioneering project that uses state-of-the-art protocols for obtaining and storing a large range of organs and tissues and for testing them in the lab. Until now, no project has analyzed genetic variation and expression in as many tissues in such a large population as planned for GTEx.</p> <p><b>Scientific Description</b></p> <p>Understanding the role of variation in the human genome is crucial to elucidating genetic contributions to human health and disease. Despite the results of genome-wide association studies (GWAS) documenting strong statistical associations between genetic variation and human traits, the functional role for most of these variants is largely unexplained. Nearly 90% of these GWAS-implicated sites lie outside of protein-coding sequences, suggesting that these variants might regulate gene expression.</p> <p>The goal of the Genotype-Tissue Expression (GTEx) project is to establish a resource database in which to study the relationship between genetic variation and gene expression in reference/non-diseased tissues. The ultimate resource would include up to 1,000 post-mortem donors with several dozen tissues from each, a resource large enough to study both <i>cis</i>- and <i>trans</i>- gene expression quantitative trait loci (eQTLs). Some tissue will also be banked for additional molecular analyses.</p> <p>GTEx was funded as a 2-year pilot project by the NIH Common Fund (CF), and will assess the feasibility of collecting high-quality RNA from multiple tissues from healthy donors. The project will collect and analyze RNA levels in 30 or more different human tissues from 160 postmortem donors and 5 tissues from a similar number of surgical controls. Each donor will be characterized for germline genetic variation through dense genotyping arrays.</p> <p>By treating RNA expression levels as quantitative traits, eQTLs will be identified as sites containing genetic variation that correlate with changes in RNA expression. Such eQTLs have been associated with 4%-12% of expressed human genes, and with common complex human diseases, including obesity, atherosclerosis, type 2 diabetes, Crohn's disease, and asthma. Additionally, few studies have examined the tissue specificity of eQTLs. The GTEx project will thus serve as a resource database and tissue bank for many future studies, especially for understanding the functional basis of inherited susceptibility to disease.</p> <p>It is anticipated that GTEx data will be made available through dbGaP on a periodic basis as it is generated.</p>
| phs000424.v1.p1 | EGA
Project description:Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
| S-EPMC4010069 | biostudies-literature
Project description:African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these diseases or drug response phenotypes. To fill this gap, we obtained 60 primary hepatocyte cultures from AA liver donors for genome-wide mapping of expression quantitative trait loci (eQTL) using LAMatrix. We identified 277 eGenes and 19,770 eQTLs, of which 67 eGenes and 7,415 eQTLs are not observed in the Genotype-Tissue Expression Project (GTEx) liver eQTL analysis. Of the eGenes found in GTEx only 25 share the same lead eQTL. These AA-specific eQTLs are less correlated to GTEx eQTL in effect sizes and have larger Fst values compared to eQTLs found in both cohorts (overlapping eQTLs). We assessed the overlap between GWAS variants and their tagging variants with AA hepatocyte eQTLs and demonstrated that AA hepatocyte eQTLs can decrease the number of potential causal variants at GWAS loci. Additionally, we identified 75,002 exon QTLs of which 48.8% are not eQTLs in AA hepatocytes. Our analysis provides the first comprehensive characterization of AA hepatocyte eQTLs and highlights the unique discoveries that are made possible due to the increased genetic diversity within the African ancestry genome.
2020-03-27 | GSE147628 | GEO
Project description:First whole tissue colon proteome for mouse
2011-03-18 | PRD000406 | Pride
Project description:The Genotype-Tissue Expression (GTEx) project is a collaborative effort that aims to identify correlations between genotype and tissue-specific gene expression levels that will help identify regions of the genome that influence whether and how much a gene is expressed. GTEx is funded through the Common Fund, and managed by the NIH Office of the Director in partnership with the National Human Genome Research Institute, National Institute of Mental Health, the National Cancer Institute, the National Center for Biotechnology Information at the National Library of Medicine, the National Heart, Lung and Blood Institute, the National Institute on Drug Abuse, and the National Institute of Neurological Diseases and Stroke, all part of NIH. This series of 837 samples represents multiple tissues collected from 102 GTEX donors and 1 control cell line. In total, 30 tissue sites are represented including Adipose, Artery, Heart, Lung, Whole Blood, Muscle, Skin, and 11 brain subregions. RNA-seq expression data, robust clinical data, pathological annotations, and genotypes are also available for these samples from dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424.v2.p1) and the GTEx portal (www.broadinstitute.org/gtex). While GTEx is no longer generating Affymetrix expression data, donor enrollment continues and is expected to reach 1,000 by the end of 2015. Updates to the GTEx data in dbGaP and the GTEx Portal will be made periodically. contributor: GTEx Laboratory, Data Analysis, and Coordinating Center (LDACC) contributor: The Broad Institute of MIT and Harvard (LDACC PIs: Kristin Ardlie and Gaddy Getz) GTEx samples are collected from deceased donors at low post-mortem intervals and preserved in PAXgene fixative prior to DNA and RNA extraction.
2013-04-09 | E-GEOD-45878 | biostudies-arrayexpress
Project description:The Pan-Cancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify common patterns of mutation in more than 2,800 cancer whole genomes from the International Cancer Genome Consortium. Building upon previous work which examined cancer coding regions, this project is exploring the nature and consequences of somatic and germline variations in both coding and non-coding regions, with specific emphasis on cis-regulatory sites, non-coding RNAs, and large-scale structural alterations. Read more on the <a href=\"https://dcc.icgc.org/pcawg\" target=\"_blank\">project website</a>.<br>This is a subset featuring RNA-seq transcription profiling data of 27 cancer subtypes in 19 tissues. Some donors have matched normal tissue. As general reference, a subset of normal tissue samples from the GTEx project were included in this experiment.
2020-02-05 | E-MTAB-5200 | biostudies-arrayexpress