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.
First, open the linear tree diagram by clicking on the appropriate link on the main Atlas page:
You will now 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.
- 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.
- 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 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 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.