This article contains instructions for accessing controlled GTEx/TARGET/TCGA data.
The National Cancer Institute's Genomic Data Commons (GDC) provides researchers and medical practitioners with a way to integrate their data with landmark studies such as the Genotype Tissue Expression project (GTEx), the Therapeutically Applicable Research to Generate Effective Treatments initiative (TARGET), and The Cancer Genome Atlas (TCGA).
The GDC requires authentication through the database of Genotypes and Phenotypes (dbGaP) and eRA Commons authorization to access controlled data. To gain access to these data, you need to request access to dbGaP by following the instructions on this page. If you don't have eRA Commons access, you can find links to help with this on the same page.
Linking your NIH account to your Terra account
Once you're in your profile section, on the left you'll see a set of options for linking to external servers. Select the option to link to your NIH account, and log in where prompted:
Once you've linked your account, you can confirm your link is active in your profile section:
Accessing specific studies
Once you've linked your Terra account, you can access the data for your study of choice through the Terra platform. Below are links to pages where you can log on to your desired resources, as well as links to where you can find relevant workspaces for those resources
The Genotype-Tissue Expression (GTEx) compiles data on tissue-specific gene expression and regulation. To access this data, follow the links below:
The Therapeutically Applicable Research to Generate Effective Treatments initiative (TARGET) aims to characterize alterations in both gene expression and genomic structure involved in childhood cancers. To access this data, follow the links below:
- TARGET access request page
- Introduction to TARGET data Terra workspace
- TARGET Acute Myeloid Leukemia (AML) Project Terra workspace
- TARGET Kidney Tumors Project Terra workspace
- TARGET Neuroblastoma Project Terra workspace
- TARGET Osteosarcoma Project Terra workspace
The Cancer Genome Atlas is an effort to coordinate data such as gene expression, copy number variation and clinical information in an effort to accelerate understanding of the molecular bass of cancer. There is a separate article here on accessing TCGA data, and you can also use the links below:
- TCGA access request page
- Introduction to TCGA Terra workspace
- List of TCGA-related workspaces on Terra
Authorization domains and troubleshooting
- Making sure your access is active in dbGaP
- Making sure you have access to the correct study
- Making sure your NIH account link is active at https://app.terra.bio/#profile (you may need to renew your account linkage, or even try unlinking and then relinking)
- Making sure you see "Authorized" for the dataset in question:
If you do not see your NIH account as being authorized for your study of interest, and you can't apply for access yourself, your PI can designate you as a downloader for the study. Once they designate you, your authorization should show up in Terra. Note that the NIH allowlist refreshes daily, so you may need to wait up to one day to see the authorization.