GTEx Portal

The Genotype-Tissue Expression (GTEx) Portal aggregates a rich, cross-tissue resource for researchers who need tissue-resolved gene expression and regulatory maps tied to donor genotypes. The core Adult GTEx collection includes matched whole-genome (WGS/WES) and bulk RNA‑seq data from nearly 1,000 deceased donors and samples from up to 54 non-diseased tissue sites, enabling genome-wide identification of expression quantitative trait loci (eQTLs), isoform usage, and tissue-shared versus tissue-specific regulatory effects. GTEx has expanded into developmental (dGTEx) and non-human-primate (NHP-dGTEx) efforts to enable temporal and cross-species comparisons of how genetics influences transcription during development. The portal exposes multiple data modalities and visualization tools. Primary molecular assays in GTEx include WGS/WES, bulk RNA‑seq, and derived QTL calls; additional assays and derived tracks available for exploration include H3K27ac ChIP‑seq, m6A methylation, whole‑genome bisulfite sequencing (WGBS), histology images, and subsets of tissues profiled with single-cell and spatial transcriptomic methods. Interactive features include gene/tissue expression browsers, single‑cell expression lookups, transcript and isoform visualizers, a Locus Browser for exploring candidate QTLs near genes, and an IGV Browser view for tissue‑specific eQTLs and read coverage. The portal also supports batch queries of eQTLs by gene and tissue and links tissue sample sites to common coordinate frameworks such as HuBMAP for anatomical mapping. Typical use cases span variant interpretation, mechanistic follow-up, and resource planning. Clinicians and geneticists use GTEx to interpret non‑coding GWAS hits by checking whether disease‑associated variants are eQTLs in relevant tissues, to prioritize candidate target genes, or to examine tissue specificity of genetic regulation. Molecular biologists use the Transcript/isoform viewers and IGV coverage tracks to design RT‑PCR assays or validate splice isoform differences. Computational biologists leverage the bulk and single‑cell expression matrices and eQTL catalogs for cross‑tissue co-expression and co-regulation analyses, and integrative studies with epigenomic annotations (ChIP‑seq, WGBS, Hi‑C) to map regulatory elements. The dGTEx and NHP‑dGTEx projects expand these capabilities by providing developmental stage–specific and cross‑species datasets (including multiome snRNA+ATAC, spatial transcriptomes, and deeper sequencing) to study how genetic control of expression changes with age or between primate species. Data access and integration are designed for both quick exploration and deeper analysis. Open‑access data such as expression counts, summary eQTLs, and many visualization tracks can be browsed and downloaded directly from the portal for programmatic or manual analyses. Protected raw sequence data and extensive donor metadata require controlled‑access requests through dbGaP and related governance, and GTEx provides protocols, quality‑control descriptions, and method documentation to support reproducible analyses. Researchers can also search and request GTEx biospecimens held in the biobank for experimental follow‑up. The portal’s outputs are routinely used in combination with other community resources (for example, ENCODE annotations and anatomical mapping frameworks) and provide citation guidance to ensure proper attribution. For most workflows, the recommended path is to explore gene/tissue expression and eQTL snapshots on the portal, inspect loci with the Locus and IGV Browsers, download summary data for computational analyses, and—if needed—apply for controlled access to raw sequence data or request biospecimens for experimental validation.