About Rna-Seq Data From Cell Lines

Question

[alittleboy]

I am currently analyzing some RNA-Seq data from different cell lines, but I think I lack basic knowledge in this area. Are there any related papers/online tutorials on this subject? For example, I'd like to know if different cell lines are from different subjects, how to deal with technical replicates of a cell line, under what situations can I compare different cell lines to see if there is, say, differential exon/isoform usage, and questions like that... Thanks a lot!!

Answer 1

[Devon Ryan]

"I'd like to know if different cell lines are from different subjects"

You'll have to look up the history of the cell lines. Some of that might be documented by ATCC, otherwise you'll have to look things up in pubmed.

"how to deal with technical replicates of a cell line"

Concatenate them together.

"under what situations can I compare different cell lines to see if there is, say, differential exon/isoform usage"

When you have biological replicates (usually meaning from different dishes) of at least one of the cell lines. It'd be easier if they were from the same organism and not hybrids.

[Devon Ryan]

See also GenoMax's reply on SEQanswers: http://seqanswers.com/forums/showthread.php?t=31337