RNA partially degraded?

Use this category for the exchange of ideas, methodologies and references regarding the isolation, manipulation and analysis of RNA. (Extraction protocols, Northern Blot analysis, RNase Protection, Differential Display, In Vitro Transcription, etc.)

Moderators: mchlbrmn, Abhijeet Bakre

RNA partially degraded?

Postby mobio7 » Jun 15 2016 5:13 am

Hi, the samples are not yet DNAse treated but was wondering what is the lowest brighter band (is it loading dye)? Is RNA partially degraded or completely degraded? Can these be DNAse treated and send for RNA-seq?
You do not have the required permissions to view the files attached to this post.
mobio7
newcomer
newcomer
 
Posts: 3
Joined: Jun 09 2016 2:32 am

Re: RNA partially degraded?

Postby r.rosati » Jun 17 2016 1:26 pm

I'm afraid your samples look degraded; however RNA-seq usually calls for a more in-depth analysis of RNA quality, such as running the RNAs on a Bioanalyzer/Tapestation.
If they are irreplaceable, they "might" still be used for RNA-seq; but at the very least you'll need to use a rRNA depletion strategy that will specifically work on degraded rRNA.
r.rosati
ModSquad
ModSquad
 
Posts: 2136
Joined: Nov 04 2002 10:23 am
Location: Brazil

Re: RNA partially degraded?

Postby mobio7 » Jun 17 2016 2:36 pm

Thanks for your reply. What do you mean by RNA depletion strategy?
mobio7
newcomer
newcomer
 
Posts: 3
Joined: Jun 09 2016 2:32 am

Re: RNA partially degraded?

Postby r.rosati » Jun 20 2016 12:38 pm

A big part of the RNA in a cell is ribosomal (the exact two bright bands there), so it is common to remove rRNA (ribosomal RNA) from the RNA pool before performing a transcriptome sequencing experiment.
What was your planned protocol?
r.rosati
ModSquad
ModSquad
 
Posts: 2136
Joined: Nov 04 2002 10:23 am
Location: Brazil


Return to RNA Methods

Who is online

Users browsing this forum: No registered users and 1 guest