I am in the process of preparing AML cell lines to do GEP analysis in three different conditions. I'll be grateful if anyone had experience with this technique to give advice about a suitable protocol to follow to get a suitable reliable results.
You can use transcriptome or whole exome sequencing by using Next-Generation Sequencing system for all your three different conditions and compare the expression patterns of them with each other.
Sercan
An Ideal experimental plan will be purely depend on the technology of choice and variables. To our experience, deep sequencing based approach is ideal. Our suggestion would be to do both RNA Seq and small RNA sequencing. This suggestion is for reasons, you would get to understand the transcriptional and post transcriptional dynamics (miRNA mediated mRNA regulation), Splicesome, LincRNAs, other small RNA and its regulatory role coupled with differential gene expression at both mRNA and miRNA level. Further, we have experience in also doing integrome analysis to identify key pathways regulated by genes and targeting miRNA . You can refer to the list of publications in RG as well as Bionivid Website www.bionivid.com , where you might get a broad idea on how we can plan the whole study. Please feel free to contact any time in case if you have any queries.
Dear Sercan and Madavan, Thank you very much for your kind and informative comments. In fact, I am interested in the role of miRNA in addition to the mRNA expression profile in AML.
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