Viewing Selected Biosamples in Grid via Faceted Search

You can find the faceted search on the Atlas home page. There are many ways to reach it:
  • Click the banner at the top of any page on the Atlas
  • Click the "Home" button in the navigation bar at the top of any page on the Atlas
  • Click Select Profiles in the navigation bar and then click Faceted Charts

It is easy to select specific types of biosamples via our faceted donut charts. There are four different categories which you can use for your selection:

You can select exRNA profiles by clicking the slices or names of facets in the charts.
  • If you want to select all possible facets, you can click the icon in the floating menubar.
  • To deselect any selected facets, click the icon in the floating menubar.
  • As you select facets, the total number of selected samples will be displayed in red above the charts.

Example: If I wanted to select biosamples that were either plasma or serum and were tagged as Alzheimer's disease, I would click the "Alzheimer's", "Plasma", and "Serum" facets.
Because 52 samples (as of July 28th, 2016) qualify for these facets, (52 selected) will be displayed in yellow above the faceted charts.
Then, in order to generate my grid, I would click the icon in the floating menubar.

Clicking this icon will create a grid that looks like the following (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.
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.

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
present in the Genboree Workbench. To learn more about this option, view this tutorial.

Also available in: HTML TXT