Viewing Summary Grid of exRNA Profiling Studies

The exRNA profiling studies grid contains a summary of various studies deposited to the Data Coordination Center (DCC).
In order to view the grid, click the relevant link on the main Atlas page:

Alternatively, you can view this summary grid by clicking the Datasets item in the menubar in the top of the atlas page:

When you click this link, you will see a grid that looks like the following:

You can click an ID under the Analysis Accession ID column to view some basic information about the given Study
including the reference genome, data analysis type, and tool name (and version) used for the analysis:

Upon clicking the icon, the RNA profile summary for that Analysis will open in a new window
(split up into two separate pictures, each depicting half of the grid):

This RNA profile grid contains a summary of reads for each biosample at various stages of mapping.
After the read count columns, there are a number of additional columns (seen in the second picture) that are described below:

ERCC Quality Standards?

  • The grid will display ERCC quality standard metrics for each sample.
    The "Meets Standards?" column will clearly indicate whether the sample meets the required quality thresholds: "YES", "NO", or "NA".
    A value of "NA" indicates that we are currently reevaluating that sample's quality.
    You can view the ERC Consortium QC Standards page to learn more about the QC standards used.

Download Data

  • Click the icon to download the exceRpt processed core results archive, with mapped read counts for various RNA types.
  • Click the icon to download the raw FASTQ file associated with the biosample.
    This icon will only be present if the dataset is already available in a public domain archive like SRA or GEO.
  • If you see , this icon means that the data is restricted access and is currently under the protected period (embargo).
    The embargo on this dataset will end 12 months after the time the data was submitted to the DCC. View the ERC Consortium Data Access Policy for more details.
  • If you see , this icon means that the data is deposited in the controlled access dbGaP archive.
    You can click the icon under the Actions column to view the dbGaP Study Id. You can then contact the PI through dbGaP to get access to the raw FASTQ data files.

Download Metadata

  • Click the icon to download the biosample metadata document associated with the biosample.
    You can also view the document in GenboreeKB (our UI for viewing metadata) by clicking the biosample's accession ID in the Biosample Metadata Accession column.
  • Click the icon to download the experiment metadata document associated with the biosample.
  • Click the icon to download the donor metadata document associated with the biosample.
Actions
  • Click the icon to view a histogram of read counts mapped to various libraries.
  • Click the icon to view information about external databases associated with the biosample.
    If the biosample can be found in any external databases (SRA, dbGaP, GEO, etc.), then a link is provided.
    If the biosample is still embargoed, then information about the embargo period is displayed, along with a link to the ERCC data access policy.

Finally, there are three additional buttons at the top of the grid.
First, the Back to Search Page button will take you back to the exRNA Atlas landing page.
Second, the Download All Samples button will allow you to download result files in bulk.
To learn more about this option, view this tutorial.
Third, the Go to Genboree Workbench button will allow you to take samples from the exRNA Atlas and feed them into downstream and comparative analysis tools
present in the Genboree Workbench. To learn more about this option, view this tutorial.

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