Principal Investigator:

Contributors: Aleksandar Milosavljevic, Mark Bender Gerstein

The DMRR SOC will 1. provide the scientific community with user-friendly, publicly accessible ExRNA information, and 2. make the scientific community aware that this information is available for their use.  Anticipated activities of the DMRR SOC include:

1. Establish and maintain a public website which will include an ExRNA Atlas.

  • The Atlas will describe subcellular production pathways, tissues of origin, principle binding partners and/or cofactors, principle cargo constituents, and potential cellular or pathway targets of specific ExRNA populations from “normal” human body fluids.
  • Included in the Atlas will be an “E-Manual” of validated and standardized Extracellular RNA protocols (isolation, manipulation, RNA-seq, etc) to be updated as protocols and technologies improve.
  • The Atlas will contain information about common reagents, useful separation biomarkers, quality control standards, standard cell line/producer line, gold standard reagents, etc to ensure lab-to-lab consistency in ExRNA preparations.
  • The Atlas should provide access to videos and tutorials (generated by the DMRR in collaboration with the ERCC PIs) on ExRNA biology, the use of ExRNA datasets and protocols, and related issues to help educate the scientific and lay community on these topics.
  • The Atlas should provide user-friendly access to datasets generated by the consortium, provide ExRNA profiles/signatures of healthy individuals, provide access to ExRNA biomarker datasets, and provide access to other relevant available datasets generated by non-consortium researchers.
  • The Atlas will be the primary portal for the broad scientific community to access ERCC data prior to publication and should provide access to “apps” as well as more sophisticated tools to facilitate data mining by both novice and experienced researchers.  The Atlas should provide access to useful software developed by the ERC Consortium and other researchers.
  • The Atlas should describe all of the datasets available for the ERCC and have metadata-enabled querying of the data to identify data subsets of interest.  Links should be provided to a description of the data including any metadata associated with an experiment.  The Atlas should provide a method to freely download large datasets so that users can acquire and analyze all or large parts of the data.  The Atlas should support data retrieval for any ERCC data deposited in NCBI or other public databases.
  • The Atlas should provide a genome browser view of the ExRNA data generated by the ERC Consortium, and should strive to make the visualization of the data as intuitive and user-friendly as possible.
  • The Atlas should improve during the course of the project.  Applicants should describe plans to solicit user feedback and otherwise evaluate the usability of the Atlas that serve the user communities, as well as to facilitate analysis of usage (quantitation of page views, FTP downloads, etc.).   This plan should describe the frequency of these evaluations and how this information will be used to improve the utility of the Extracellular RNA Atlas to the user community.

2. Develop an outreach strategy to advertise available ERCC protocols and resources to the scientific community.  The outreach strategy should include:

  • sponsorship of workshops open to scientists outside of the consortium to facilitate use of datasets.
  • support of sessions at scientific meetings to advertise ERCC discoveries and resources.
  • establishment of a discussion forum to engage the scientific community interested in this topic.
  • utilization of appropriate social media outlets for information about ERCC.