Building a Cohort within the ICDC
The Integrated Canine Data Commons is a cloud-based repository of spontaneously-arising canine cancer data from pet dogs established to further research on human cancers by enabling comparative analysis with canine cancer. All files available through the ICDC are open-access and can be exported to the CGC by any user. For this tutorial, we will conduct an example RNA-Seq analysis using 6 Binary Alignment Mapping (BAM) files derived from 6 canine individuals enrolled in the UBC02 study. 3 files are from tumor tissues sequenced from diseased individuals and 3 files are from normal tissues sequenced from healthy individuals.
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The ICDC has a comprehensive menu of faceted values that can be used to filter data by cases, sample, and files. For example, data can be filtered by the disease diagnosis, the sample pathology, or file format. Specific cases of interest can be found entering the case IDs or uploading a list of case IDs. For this tutorial we will filter by the UBC02 study and select cases that are associated with multiple studies.
Step 1: Filter cases using faceted search
- Navigate to the ICDC Explore Dashboard
- Expand the Study facet and select UBC02
- Expand the Study Participation facet and select Multiple Study
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The ICDC Dashboard makes it very simple to load files of interest into the "My Files" Cart page. After applying desired filters, either click on the Add Files for All Cases button to add files for every case listed in the Dashboard table or explicitly select cases of interest by clicking on the checkboxes and then click on the Add Files for Selected Cases button. For this tutorial we will select a total of 6 cases and add files for those cases.
Step 2: Add files to the Cart
- From within the Dashboard table click on the checkbox corresponding to 3 healthy controls and 3 diseased canines
- Click on the button
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The ICDC "My Files" Cart page enables users to view files of interest in JBrowse, a next generation genome browser, export these files to the CGC, and/or download a file manifest containing metadata describing each file to their local computer. For this tutorial, we will be exporting our files directly to the CGC.
Step 3: Export files in the Cart to the Cancer Genomics Cloud (CGC)
- Click on the My Files icon in the top right of the navigation bar
- Check to make sure there are 12 files in the cart
- Expand the dropdown menu of the button
- Click on
- Follow the prompt to login to the CGC or create an account if one does not yet exist
- Select a from the dropdown menu or create a new project using the instructions in Step 0 of the Navigating the CGC section
- Select the checkbox to agree to the CGC terms
- Click on the button
