Hi, I'm new to the sequencing world and have a few questions regarding a project I'm starting to look for expressed SNPs.
In order to maximise the number of SNPs sequenced I'm thinking about looking at pre-mRNAs, so currently I'm performing nuclear fractionation. My question is whether it would be better to do a ribosomal depletion (Invitrogen ribominus kit) or polyA selection? Has anyone had positive/negative experiences with these protocols and how easy is it to call SNPs from libraries prepared this way?
Any advice/comments would be greatly appreciated!
~Mel
In order to maximise the number of SNPs sequenced I'm thinking about looking at pre-mRNAs, so currently I'm performing nuclear fractionation. My question is whether it would be better to do a ribosomal depletion (Invitrogen ribominus kit) or polyA selection? Has anyone had positive/negative experiences with these protocols and how easy is it to call SNPs from libraries prepared this way?
Any advice/comments would be greatly appreciated!
~Mel
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