a question about non coding RNA sequencing data

[Julia Sidorova]

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

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[debr...@mskcc.org]

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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