Viewing Selected Biosamples in Grid via Linear Tree

You can use our dendrogram-like partition diagram ("linear tree") to interactively drill down into different subsets of biosamples.
There are two ways of reaching the linear tree page:
  • Click the Select Profiles button in the navigation bar and then click the Linear Tree Drill-Down button.
  • Go to the Atlas homepage and click the Linear Tree Drill-Down link in the Browse exRNA Profiles - Alternative Options panel.

After you open the linear tree drill-down page, you will see a diagram like the following:

Click on a collapsed node to "drill down" along its path in the Anatomical Locations » Biofluids » Conditions facet sequence.
  • Click on an expanded node to collapse it.
  • Reset/clear your active path using the icon in the floating menubar.

Your selected path is always clearly highlighted:

Clicking the icon in the floating menubar will open the search results for your particular drill-down path (split up into two separate pictures, each depicting half of the grid):

In the first picture above (which displays the first half of the grid), we see each biosample's name as well as some key metadata properties
of each biosample (Condition, Anatomical Location, Biofluid Name, and exRNA Source).

In the second picture above (which displays the second half of the grid), we see the following information and links:

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

  • For all profiles, click the icon to download the "core processed results" associated with the sample.
    • For RNA-seq profiles, this download will be the exceRpt processed core results archive.
      This archive will contain mapped read counts from all three stages of exceRpt (endogenous, exogenous miRNA and rRNA, and exogenous genomes).
    • For qPCR profiles, this download will be the qPCR Targets file. The file will contain different miRNA targets and associated Ct values for those targets.
  • For RNA-seq profiles, click the icon to download the full results (alignments) for the first two stages of exceRpt (endogenous alignment and exogenous miRNA and rRNA alignment).
  • For RNA-seq profiles, click the icon to download the original FASTQ source file.
  • 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 (or will be soon) into a controlled access archive like dbGaP.
    You can click the icon under the Actions column to view any available links to controlled access archive(s) that contain data for the relevant biosample.
    You can then request access through those external databases.

Download Advanced Results

  • For RNA-seq profiles, click the icon to download the taxonomy tree (either exogenous ribosomal RNA or exogenous genomic reads) created by exceRpt.
  • For RNA-seq profiles, click the icon to download the full results (alignments) for the third stage of exceRpt (exogenous genomic alignment).
  • 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 (or will be soon) into a controlled access archive like dbGaP.
    You can click the icon under the Actions column to view any available links to controlled access archive(s) that contain data for the relevant biosample.
    You can then request access through those external databases.

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.
  • Click the icon to download a file containing all three metadata documents (biosample, donor, and experiment) associated with the biosample.

RNA Profile

  • Click the icon to view a histogram of read counts mapped to various libraries.

External References

  • 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.
  • Click the icon to open the PubMed page associated with the biosample.
    If there is no PubMed page, you will get a pop-up alerting you that no references could be found.

There are three additional buttons at the top of the grid.
First, the Back to Home 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 Analyze Selected Samples button will allow you to take samples from the exRNA Atlas and feed them into downstream and comparative analysis tools.
To learn more about this option, view this tutorial.

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