Accessing GTEx/TARGET/TCGA data

Anton Kovalsky
  • Updated

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've been granted the necessary permissions, to be able to interact with the data through Terra, you'll need to link your Terra account to the NCI CRDC Framework Services. To do this, open the main Terra menu on the Terra landing page, click on your name, and then click "Profile" underneath your name:

 

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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:

 

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Note: If you are seeking access to TCGA data, you will also need to be linked to the NCI CRDC Framework Services. You can link using your same NIH credentials.
 
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Once you've linked your account, you can confirm your link is active in your profile section: 

 

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Terra will give you a reminder in the UI when your link is close to expiring.
 
 

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

GTEx

The Genotype-Tissue Expression (GTEx) compiles data on tissue-specific gene expression and regulation. To access this data, follow the links below:

TARGET

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:

TCGA

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:

 

Authorization domains and troubleshooting

Authorization domains for each dbGaP resource are set to automatically sync with the allowlist from NIH/dbGaP on a daily basis. These lists aren't manually managed and all depend on dbGaP seeing you as a user with access to the data. As such, if you get access to one of the datasets that day, you might not be able to get access to the data through Terra until the next day, when the system automatically updates. If you've done everything properly but are having trouble accessing data, a few things you can try to troubleshoot your situation before contacting support include:
  • 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:

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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.

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