Problems with low input single-cell RNA-seq

adamreid

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Join Date: Nov 2009

Posts: 6
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Problems with low input single-cell RNA-seq

02-12-2016, 01:16 AM

We are trying to sequence RNA from individual small cells.

We are sorting by FACS and using SmartSeq2 and Nextera XT to make libraries.

We have had several problems.

We get rRNA contamination from both E. coli (perhaps due to contaminated reverse transcriptase) and from our target organism. This is strange because SmartSeq2 should only amplify polyA mRNAs.

Secondly when we sequence the libraries we get adaptor contamination, sometimes from the strand-switching oligo and also from the Nextera transposase.

Has anyone noticed similar problems?

Cheers,

Adam
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nucacidhunter

Jafar Jabbari

Join Date: Jan 2013

Posts: 1250
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02-12-2016, 02:01 AM

I would suggest you post in the following thread:

Just a moment...

http://seqanswers.com/forums/showthread.php?t=9967&highlight=single+cell+rnaseq
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Problems with low input single-cell RNA-seq

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