Hello,
it may be a naive question, but here it goes: we are interested
in accessing RNA expression levels of pericentric satellites OR
satellite DNA copy number in the TCGA datasets. We want to compare
the levels of SAT transcripts or SAT copy numbers in cancers
vi-a-vis a the level of the protein ATAD2. The question is, are
non coding RNA reads and/or repetitive DNA reads mapped in a
typical dataset? And if not, can we download ALL reads and do our
own mapping? We are specifically interested in the 594 sample
Colorectal Adenocarcinoma Pancancer Atlas dataset.
Thank you,
Julia
Hi Julia,
Thanks for reaching out!
Just a caveat: I am not very familiar with satellite analysis but I will try to give an answer. There are some non-coding RNA genes in the TCGA Pancan dataset of cBioPortal, see e.g. MALAT1. So you can maybe confirm by querying some of the SAT transcripts you are interested in.
If they are not available, one could check if the SAT transcript expression or copy numbers are provided in the datafiles on GDC somewhere. Only if they are not there one could indeed try to download the reads and do your own mapping. The sequencing reads can be downloaded on GDC as well
Hope that helps a bit! Hoping anyone else on the mailing list can chime in with additional information
Thanks!
Ino
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