I was going to mix antisense oligos, directed against the start codon region of the mRNAs I want to remove, and RNase H into purified total ply(A) mRNA. I'm thinking this approach is a bit sloppy, though, and I'd have to validate ~200 oligos. I was wondering if there was an easier way:
My transcriptome of interest contains roughly 15000 different transcripts, so piecing together a new transcriptome, without the 200 transcripts I want to remove, isn't feasible.
Edited by Ahrenhase, 22 October 2013 - 10:19 AM.