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Old 01-12-2009, 08:08 PM   #3
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Location: Switzerland

Join Date: Aug 2008
Posts: 116

Originally Posted by Eshchar View Post
Hi all,

Regarding RNA preparation for mRNA seq (we are using Illumina), we are using Qiagen's Oligotex kit for poly-T selection. So far we have observed that in the final sequencing, approximately 40% of our short reads are ribosomal RNA derived.

Can people perhaps share how much rRNA sequence is present in their Illumina RNA seq runs, and what sort of mRNA selection are they using?

Also, are any users familiar with the of Ribo-minus rRNA depletion kit from Invitrogen?
I have tried Oligotex kit but not satisfied with the quality of cDNA synthesized (probably due to degradation). Have you tried two rounds of oligo dT priming using Dynabeads mRNA purification kit as recommended in the mRNA-seq protocol?

Check out Brian's reply at the following link

Hope this helps.
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