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-   -   Need help interpreting these weird Bioanalyzer results (http://seqanswers.com/forums/showthread.php?t=40389)

Sciurus 01-29-2014 06:06 AM

Need help interpreting these weird Bioanalyzer results
 
1 Attachment(s)
Hi everybody,

Today, I extracted RNA from plant material, which I want to - eventually - sequence. For quality check I ran them on the Bioanalyzer as I have done several times with the same type of samples and always had good results (high RIN, nice peaks, etc.) but this time it came out very weird... Lots of smear in some, in others almost nothing.
I attached the whole output pdf, so maybe - please - someone here knows if this is my samples or the Chip or whatever?

Thanks already! :-)

flobpf 01-29-2014 07:03 AM

Looks like RNA fragmentation or DNA contamination to me. The peaks are well correlated with the gel. If it was the chip, you'd have seen it across all samples. You might want to run an agarose gel yourself to confirm fragmentation. Maybe the DNAse treatment step was not very efficient? Or you didn't completely inactivate RNAse...

Sciurus 01-29-2014 07:10 AM

I didn't do DNA-free treatment yet. But I hadn't done before either when the results were good.
I was suggested that the RNA hadn't completely resolved in the buffer. Can that be?

flobpf 01-29-2014 07:15 AM

Quote:

Originally Posted by Sciurus (Post 131102)
I didn't do DNA-free treatment yet. But I hadn't done before either when the results were good.
I was suggested that the RNA hadn't completely resolved in the buffer. Can that be?

If that was the case, I think you'd see lighter bands and lower RNA yields. You wouldn't see new bands.

Sciurus 01-29-2014 07:18 AM

Quote:

Originally Posted by flobpf (Post 131106)
If that was the case, I think you'd see lighter bands and lower RNA yields. You wouldn't see new bands.

Okay, thanks! So, you'd say it's DNA contamination?

flobpf 01-29-2014 08:04 AM

or RNA fragmentation due to incomplete inactivation of RNAse from sample.


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