Need to conduct gene expression studies using cell lines (treated with a drug vs. no treatment). Is one method better than the other? Cost is a consideration too. Also want to know how many samples should I run for each group (treated vs. no treatment).
Hi Cheng,
I think RNA seq will be the best in case to find out candidate genes that express or reduce in the effect of the drug. RNA seq will give you platform to do various other things like gene ontology, differential expression profile, orthology profile and many more. See this article- Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews Genetics. 2009;10(1):57-63. doi:10.1038/nrg2484.
Gene chip is more old school technique and doesn't have the platform to do all this analysis. Mostly, you can get a heat map out of it showing the differential expression. It will be inexpensive than RNA seq.
But I will suggest RNA seq will be best for your research question.
Dear Cheng,
in principal, both techniques can be used. I disagree to the comment above in the sense that you can do GO and differential gene expression with chips as well!
If you do not need to look at differential splicing etc., and have a look at the costs, the microarrays will do the job smoothly, since also the computing is far more easy than with next gen.
Concerning the groups I would suggest triplicates.
Dear Cheng, I mostly agree with the previous message. If you know what biological pathways are of interest and are not interested in an whole transcriptomic view of drug induced changes, you can go for microarrays. If you want a more detailed analysis, then you can choose RNA-seq, but it demands some investments in time for analysis, although post sequencing providers now include analysis in their offers. The most recent generation of microarrays is said to be as good as RNA-seq in terms of gene coverage, detection of differential splicing and so on, but I never used them, and they are almost as costly and as difficult to analyze... if you want it quick, simple and cheap, go for a good old affymetrix or other well known "old generation" microarray and it will do the job, as long as you are working with a well known organism (human, mouse or rat). Since you're working with cell lines and therefore are not restricted in terms of material (not animals, no precious primary sample from patients), I would suggest al least 5 replicates in each group. Good luck!
Thanks! I have a target already and would like to know what leads to upregulation of this target and if similar targets are also upregulated. So the Affy microarray may be sufficient.
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