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Seminar October 2022

Published on 10 October 2022

Start Monday October 10th (new date) at 4pm (CEST, Berlin/Paris)

(3 pm London/Lisbon, 10am New-York, 7am San Francisco, 5pm Tel Aviv)

Link to the Zoom conference:

Link to the YouTube stream: Useful to check starting time in your time zone

Main Speaker: Marc Friedländer, Associate professor, Principal investigator in quantitative RNA biology, Stockholm, Sweden (Link)

Title: agoTRIBE experimentally maps microRNA targets transcriptome-wide in single cells


MicroRNAs are gene regulatory molecules that play important roles in numerous biological processes including human health. The function of a given microRNA is defined by its selection of target transcripts, yet current state-of-the-art experimental methods to identify microRNA targets are laborious and require millions of cells. We have overcome these limitations by fusing the microRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing for the first time the detection of microRNA targets transcriptome-wide in single cells. Our agoTRIBE method reports functional microRNA targets which are additionally supported by evolutionary sequence conservation. As a proof-of-principle, we study microRNA interactions in single cells, and find substantial differential targeting across the cell cycle. Lastly, agoTRIBE additionally provides transcriptome-wide measurements of RNA abundance and will allow the deconvolution of microRNA targeting in complex tissues at the single-cell level.

Short session speaker (8 minutes long): Matthias Zytnicki, senior researcher, Toulouse, France (Link)

Title: 4 tools for small RNA-seq (mapping, quantification, differential expression)


I will present 4 tools I developed for smallRNA-Seq.
Namely, these tools include:
 - a mapping tool (srnamapper), which finds all the optimal hits;
 - two quantification tools (mmquant and mmannot), which assess the expression of the genes;
 - a differential expression finder (srnadiff), which even works when no annotation is given.

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