RNAget

Provides a common set of communication channels to efficiently retrieve RNA data of interest

The human body contains thousands of genes that support biological activities, from initiating processes like digestion to fighting off illness. To study gene expression, researchers use RNA sequencing — a powerful technology that captures gene activity levels based on the amount of RNA present in a cell. RNA sequencing experiments, however, require anywhere between 15 to 200 million RNA segments per biological sample. Such experiments can produce massive and complex files that are challenging to parse through and difficult to manage at scale. Developed by the GA4GH Large Scale Genomics (LSG) Work Stream, the RNAget API provides a common set of communication channels that allows researchers to efficiently retrieve RNA data of interest.

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Benefits

  • Retrieves RNA data of interest, saving time and disk storage space
  • Enables interoperability and harmonisation with other institutions through common RNA data structures

Target users

Researchers

Image summary: Learn how RNAget can help researchers retrieve a specific portion of RNA sequencing data for analysis.
THEME
CATEGORY
TYPE
STATUS
Work Stream
LATEST VERSION
Product Leads
  • Sean Upchurch
  • Emilio Palumbo
Staff Contact
Tools & Platforms

Community resources

Dive deeper into this product! RNAget  describes a common set of endpoints to search and retrieve processed RNA data. Currently, the RNAget API allows for the retrieval of four data types: expression-level data based on a gene of interest; data from specific genomic coordinates; project-related information; and study-related information. The RNAget API allows the requester to specify a slice of the overall matrix for delivery — helping reduce the amount of data to transfer, and focusing data mining efforts. For the API to work seamlessly, the specification includes a testing application for servers to implement, ensuring compliance with the RNAget API.


Title

Info

Repeat

Day

Time

Duration

Working meeting focused on endpoints for search and retrieval of processed RNA data.

Meets on the third Wednesday of the month.

Monthly
Wednesday
17:00 UTC
1 Hour

Date

Version

Title

Related Driver Projects and Organisations

Canadian Distributed Infrastructure for Genomics (CanDIG)
ELIXIR Beacon
The Encyclopedia of DNA Elements (ENCODE)
Broad Institute of MIT and Harvard

Don't see your name? Get in touch:

  • Jeremy Adams
    DNAstack
  • Guillaume Bourque
    McGill University / Université McGill
  • David Bujold
    McGill University / Université McGill
  • Romain Gregoire
    Canadian Centre for Computational Genomics
  • Roderic Guigo
    Centre for Genomic Regulation
  • Ben Hitz
    Stanford University
  • Emilio Palumbo
    Centre for Genomic Regulation
  • Emilio Righi
    Centre for Genomic Regulation
  • Sean Upchurch
    California Institute of Technology
  • Andy Yates
    EMBL's European Bioinformatics Institute (EBI)
  • Zhenyu Zhang
    University of Chicago

News, events, and more

Catch up with all news and articles associated with RNAget.

8 Jul 2021
GA4GH standards in a global learning health system
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