SEQanswers

Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA_seq on (non-model) less well annotated genomes Drerio General 5 06-11-2012 12:46 AM
small rna sequencing sample quality control entomology RNA Sequencing 2 01-16-2012 04:59 PM
How to evaluate reads quality of a sample for a bacterial genome nivea Bioinformatics 0 07-11-2011 01:12 PM
RNA sample quality for 454 transcriptome sequencing rtei Sample Prep / Library Generation 3 04-23-2010 10:06 AM
% matching problem- RNA_Seq sanush RNA Sequencing 1 11-29-2009 10:58 PM

Reply
 
Thread Tools
Old 07-28-2010, 01:12 PM   #1
cub103
Member
 
Location: new orleans, la

Join Date: Feb 2010
Posts: 12
Default Sample quality for RNA_SEQ

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
Attached Files
File Type: pdf RNA Integrity_72810.pdf (282.3 KB, 51 views)
cub103 is offline   Reply With Quote
Old 07-29-2010, 03:52 PM   #2
ScottC
Senior Member
 
Location: Monash University, Melbourne, Australia.

Join Date: Jan 2008
Posts: 246
Default

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.
ScottC is offline   Reply With Quote
Old 07-30-2010, 11:13 AM   #3
cub103
Member
 
Location: new orleans, la

Join Date: Feb 2010
Posts: 12
Default

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
cub103 is offline   Reply With Quote
Old 08-02-2010, 07:26 AM   #4
josdegraaf
Member
 
Location: Germany

Join Date: Mar 2010
Posts: 33
Default

Search for DSN Normalization SamplePrep Application Note
josdegraaf is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:44 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO