Sample quality for RNA_SEQ

[cub103]

Dear all,

I am preparing samples for RNA-SEQ - total RNA was isolated from OCT-Embedded frozen tissue using trizol - I run a RNA integrity check today but there's a lot degradation in some of my samples (See attached, band 1-6). I wonder if these samples could still be used or I have to get some high quality RNA?

BTW, Would too much OCT in the samples affect the isolation process and Quality of RNA?

Thanks.

Cub

[ScottC]

Hi,

If you have degraded RNA, then you might want to consider using a method other than poly-A based enrichment (which is what most kits use, including Illumina's sample prep kit) for removing structural RNA and other highly abundant species. There is a method that utilises time- and concentration-dependant rehybridisation and a duplex-specific nuclease to remove highly abundant transcripts. If you're using Illumina sequencing, there is a tech note on it on their website. A google search should turn up the documentation that you need.

Cheers,

Scott.

[cub103]

Hi Scott,

Thanks of the information. I was not able to locate the document you mentioned - wondering if you can post a link? Thank you.

Cub

[josdegraaf]

Search for DSN Normalization SamplePrep Application Note