Problems with low input single-cell RNA-seq

[adamreid]

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

[nucacidhunter]

I would suggest you post in the following thread:

http://seqanswers.com/forums/showthread.php?t=9967&highlight=single+cell+rnaseq