SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Total RNA quality (Bioanalyzer trace attached) peromhc Sample Prep / Library Generation 26 10-12-2015 03:36 PM
RNA-seq technical replicates at library construction level obig Bioinformatics 9 08-15-2012 11:43 PM
Handmade mRNAseq library prep protocol w/ 10ng total RNA lukas1848 Sample Prep / Library Generation 0 11-02-2011 04:31 AM
total RNA quality for library construction neveaire Sample Prep / Library Generation 4 04-05-2011 11:39 AM
Total RNA quality for 454 nathanjd Sample Prep / Library Generation 0 05-24-2010 06:19 AM

Reply
 
Thread Tools
Old 08-29-2011, 07:31 PM   #1
wayland
Junior Member
 
Location: shanghai,china

Join Date: Dec 2009
Posts: 2
Default total rna quality for library construction

Hi,

I have a total RNA sample that shows this RNA pattern in bioanalizer

3VHZ[87[~TS29@@TJG6IVDY.jpg

the tRNA tatio 28s/18s is 1.3;but not show RIN values on the Agilent Bioanalyzer. other samples like this pattern have low RIN values on the Agilent Bioanalyzer,such as 6.8.

do you think that quality is ok?

thanks a lot
wayland is offline   Reply With Quote
Old 08-30-2011, 06:38 AM   #2
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,315
Default

Looks good.
If you want to see your RIN score you can check for errors in the error pane. It may be something like the "5S Region Anomaly Threshold" error. Then you can increase the 5S Region Anomaly Threshold from 0.5 to 1 and it should clear the error and give you a RIN score. But the RIN score will be unduly low due to the amount of small RNAs you have. So it is probably not worth the trouble.
--
Phillip
pmiguel is offline   Reply With Quote
Old 10-12-2011, 12:02 PM   #3
cnicolet
Member
 
Location: Los Angeles

Join Date: Dec 2008
Posts: 35
Default

Is this plant RNA? You won't get a good RIN from that, but it looks intact.
cnicolet is offline   Reply With Quote
Old 10-13-2011, 05:10 AM   #4
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,315
Default

Plant RNA per se, will not necessarily give you poor RIN scores. We have a recent set of wheat RNAs submitted that all gave RINs > 9.5.

I think, other than actual degradation, the factor that will most lower the RIN score is a high concentration of small RNAs. That is typical of some isolation methods -- the Trizol (or other acid phenol) methods allow much higher yields of low molecular weight RNAs. For some applications that is actually good (well, obviously for small RNA projects). But for normal RNAseq experiments it can cause issues.

But, yes, it is not uncommon for plants to have a bunch of weird peaks (frequently plastid rRNA).

--
Phillip
pmiguel 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 06:08 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO