Closed eboileau closed 5 months ago
eboileau
commented
8 months ago Start with
m6A GLORI - https://pubmed.ncbi.nlm.nih.gov/36302990/ (only HEK, mESC, MEFs and HeLa) eTAM - https://pubmed.ncbi.nlm.nih.gov/36593412/ (only HeLa and mESC)
Pseudouridine BID-seq - https://pubmed.ncbi.nlm.nih.gov/36302989/ (many mouse tissues including heart) PRAISE - https://pubmed.ncbi.nlm.nih.gov/36997645/ (only HEK293)
Nm-sugar modifications https://www.nature.com/articles/s41422-023-00836-w
eboileau
commented
7 months ago eboileau
commented
7 months ago Added 1998f7ba1a94bd96baf777fed0d1477823b61980. https://scimodom-beta.dieterichlab.org/ now has the above dataset.
eboileau
commented
7 months ago As for tRNA data, I need advice, and ultimately we need to see what users are doing, and what they want.
As far as I can see, Ensembl annotation should have all tRNA genes. We are using Ensembl already. So I guess this would work for the standard BED6 fields, and for annotation (gene name, ID).
GtRNAdb is also well known.
What about mt-tRNA? Do we need a special "class"?
eboileau
commented
6 months ago
Aims/objectives.
We're currently using a "mock" DB for development with a minimal number of combinations allowing to see different RNA types, modifications, etc..
For the retreat, we need a proper DB with public datasets. If we get a number of these, ideally different modifications, at least 2 organisms, different cells/tissues, different technologies, etc. If possible, a tRNA modification dataset would be great (from the FE point of view, this doesn't make a lot of difference, but for BE this might, and I'm not sure yet what are the implications, e.g. annotation, etc.).
A clear and concise description of todo items.
WP1 should take care of preparing these data in EUF. But we'll need to prepare a new DB, and see that this works fine before the retreat.