Cell Line gene expression Analysis with multiple replicates
I am looking to conduct differential gene expression analysis comparing one cell line to many others. However I would like to have multiple replicates (5+ or so) for each cell line. It is possible to download samples from many different GEO datasets, but I would have to conduct extensive data normalization to make a fair comparison, and I want to avoid that. Does anyone know of a data source (i.e. one dataset) from which I might obtain gene expression data with MANY SAMPLES PER CELL LINE? Thanks!
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I wouldn't recommend comparing expression data between different studies, as there will be myriad differences from RNA isolation to array version. Best to look at a single study that has analyzed cell lines of interest. ENCODE have analysed tons of lines in duplicate and they have high quality checking.
http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/
I second this suggestion. Normalising and correcting for technical effects will be almost impossible to do accurately if there's differences in platform, chemistry, sample prep. See my answer here if you want details on how difficult it is.