Using diff of polyA and ribozero prepped RNA?

[MG1655]

Hi all,
I'm wondering if anyone knows if there are advantages to having both polyA and ribozero prepped RNAseq data? For example, one could potentially use the diff to find non-coding RNAs?

I'm preparing an experiment with yeast and am planning on duplicates for each timepoint. I thought it might be interesting to do one set of replicates with polyA-enrichment and one set of replicates with ribozero enrichment. Not only would I still get the statistical power of duplicates, I could also get a direct measurement on non-polyA, non-ribosomal RNA. Am I wrong?

Thanks!

[snf]

There will be many differences between these two procedures that may or may not have to do with the actual polyA status of the transcripts. polyA selection generates a strong 3' bias among transcripts, depending on the quality (RIN) of the input RNA. Reports at meetings recently have indicated that the correlation between polyA selected and ribo-depleted libraries from the same input total RNA can be as low as 0.9, depending on the method used for ribo-depletion. Therefore, this could confound your method.

That said, I do think it could work, you just have to keep possible bias of the rRNA-depletion method in mind when conducting downstream analyses.