High molecular bands in RNA isolation sample

monkey_SEQ

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Join Date: Oct 2011

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High molecular bands in RNA isolation sample

02-14-2012, 04:03 PM

I am attempting a de novo transcriptome assembly and have a question about genomic DNA contamination. I have treated my RNA samples twice with DNAseI (on-column and then afterwards in solution as it seemed that there was still HMW smears present). After both these treatments I still feel that I have not gotten rid of the HMW smears (see att 1% agarose gel, RNA ladder). I don’t have primers available to definitively test for gDNA. Could somebody please comment on what these HMW smear can be?

(PS. Only a single rRNA band present as this is an insect species with a ‘hidden break' in the 28S rRNA).

What effect will contaminated gDNA sequences have on the transcriptome assembly process?

Much appreciated
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ywg

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Join Date: Feb 2012

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#2

02-14-2012, 07:41 PM

How about do a RNAase test. treat small aliquot of rRNA with RNAase. compare with and without RNAase to confirm it is real gDNA contamination?
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High molecular bands in RNA isolation sample

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