How Can I Get The Whole Gene Expression Information In One Cell Line?

Question

[pengcui1989]

Dear all, I want to get the whole gene expression information in one cell line. And I find that ENCODE has the cell line's RNA-seq information. Howerer, there are five labs doing the experiment ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=292551613&c=chr22&g=wgEncodeRnaSeqSuper). Some are long RNA-seq, And some are Sm RNA-seq and so on. I don't know which one can stand for the whole cell's gene expression information. Who can tell me how to choose? It's very kind of you!

[Michael Schubert]

There is no "one" expression profile, what is expressed strongly depends on culture conditions.

Answer 1

[JC]

Each lab was doing different experiments, if you are interested in only one measurement of gene expression in a cell line, you can select any "whole cell PolyA-selected" sample and their replicates, such as the Caltech data set.

[pengcui1989]

OK, i know that. I'm new in RNA-seq. And I also have two simple questions. (1) Many labs have two replicates. Is it OK that I choose any one? (2) What is the RNA extract? I find three kinds: total RNA, longpolyA+RNA, longpolyA-RNA. What are their differences? It's very kind of you to answer my questions!