Re-analysis of Extracellular RNA Communication Consortium data

[lpantano]

Dear miRTop colleague,

We are inviting you all to participate in an isomiR research project. We have been talking for some time about isomiR naming conventions. One of the potential challenges with isomiRs is that technical factors such as library preparation methods may skew the isomiR families. Marc is publishing on this in an upcoming Genome Research paper. We think it may be valuable to determine the extent to which biology or technical reasons impact on isomiRs of miRNAs.

To that end we have identified a dataset that we feel would be useful to solve this problem. Dr. Muneesh Tewari has graciously agreed to share data from the recent Extracellular RNA Communication Consortium (ERCC) study comparing RNA-seq of miRNAs from 9 different laboratories. The preprint is here and we encourage you to read it: http://www.biorxiv.org/content/biorxiv/early/2017/05/17/113050.full.pdf. The datasets are here, but are not yet released to the public: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=whipakmajrwprcv&acc=GSE94586. The group used a pooled plasma sample and a set of synthetic RNA libraries with multiple different library preparation methods. We believe we can use the 15 sequencing runs of the same plasma samples to ask some important questions about the etiology of isomiRs.

We can specifically address the extent of different library preparation kits on isomiR formation. We can also analyze the raw .fastq files with different miRNA alignment software to determine the role different methodologies have on isomiR calls. You likely have more ideas of what we can do with the data.

We propose to have a conference call to discuss the project for those of you who are interested. We can do some brain-storming, discuss the objectives, the methods, and settle on a division of labor based on everyone’s areas of expertise. We would like to publish a manuscript on the findings from the authorship of “The miRTop Consortium.” We believe this will give us credibility when we propose new naming conventions.

Please let us know your interest in such an endeavor. Participate in the doodle to agree on a date for the conference call: https://beta.doodle.com/poll/f59aetuganmu7hau.

Sincerely,
Lorena Pantano and Marc Halushka

[ThomasDesvignes]

This is a really great idea. We've in house tried few things (library prep kits, aligners, ...) and noticed differences in results.

[lpantano]

Thanks all for participate.

As expected I could find a time so all can be there, but we'll post minutes so the ones who cannot assist can catch up and I am happy to have a call with them. (mainly Gianvito)

The meeting will be Friday, 15th, at 10:00 AM EST time | 4:00 CEST time. I'll send link to the conference call the day before.

Looking forward to talk to you.

[mhalushka]

I encourage all participants to bring some ideas for what we'd like to (practically) understand from this data set. If anyone has additional datasets that can also be used, let's discuss those as well.

[lpantano]

Hi all,

This is the way to participate on the call:

Topic: miRTop -ERCC data
Time: Sep 15, 2017 10:00 AM Eastern Standard Time (US and Canada)

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/256856786

Or iPhone one-tap :
US: +14086380968,,256856786# or +16468769923,,256856786#
Or Telephone：
Dial(for higher quality, dial a number based on your current location)：
US: +1 408 638 0968 or +1 646 876 9923 or +1 669 900 6833
Meeting ID: 256 856 786
International numbers available: https://zoom.us/zoomconference?m=upSaM8TGiPQmKN4vZ8utcpvVRqaosy_V

[lpantano]

Thanks for join the call.
As quick minutes, we decide the following (please modify the message if I miss something):

• Marc will choose a random data set to analyze the data that will help to optimize the output from each tool to GFF format as defined here: https://github.com/miRTop/incubator/blob/master/format/definition.md
• In the next week we define the tools we want to use. Please add the information here: https://github.com/miRTop/incubator/blob/master/projects/Reanalysis_ERCC.md
• List specific question to address mainly in two categories (to be discussed in the next month):
  • broad comparison: like miRNA detected, expression, number of isomiRs
  • specific comparison: type of isomiRs

I think we'll try to keep monthly meeting to assure the continuity of the project.

Cheers