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Old 11-30-2016, 01:15 PM   #1
sjeschonek
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Location: Rhode Island

Join Date: Feb 2014
Posts: 7
Default Best library prep kit for RIP-Seq

We are preparing to do RNA-IP (RIP)-seq. For library capture in our system, we will need to do ribosomal depletion (rather than mRNA enrichment). Our input varies -- our negative control sample will have very little RNA (100 ng) whereas our experimental samples usually pull down about 1 ug of RNA.

There are so many kits available! We are leaning towards Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero, mainly because the brand is so well known, a leader in the NGS field, and has a very clear user manual. But is it really the best kit? It is certainly the most expensive (which we are able to spend if this is really the best kit).

Do others have experience with the NEBNext rRNA Depletion Kit or the KAPA RNA HyperPrep Kits with RiboErase, or any other kits? Thanks!

Also, is there a way to test these different kits (I know trial sizes are offered) without actually running samples on a sequencer?
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