We are tying to sequence and build de novo transcriptomes from total RNA for phylogenomics of non-model organisms (Lophotrochozoa), the degraded samples cannot be re-collected.
What kind of depth are you looking for? Are you doing a shearing/size selection step?
It might be a good strategy to do random hexamer priming instead of polyA. Degraded RNA transcripts will lose their polyA tails first, you'll able to salvage more transcript with hexamers.
To deal with ribo RNA ithout a ribo depletion kit, you might be able to remove some of it by doing a size selection step (beads or gel) before shearing the cDNA. That will probably get rid of some of it and you may be able to bioinformatically remove the remaining ribosomal reads from your downstream data
Good luck
Many thanks! We'll be looking at about 50-60 million paired end reads on Hiseq, haven't selected a size selection step yet as had some information that it was sensitive to RNA fragmentation.
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