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Old 11-17-2016, 10:47 PM   #1
Junior Member
Location: Kenya

Join Date: Nov 2015
Posts: 5
Question Scriptseq insystem contamination

I have recently begun using the scriptseq complete gold epidemiology kit to sequence RNA from human blood samples. From the number of runs I have done, I have consistently seen hits from the following Avian myeloblastosis associated virus AND Bacillus subtulis/sp. I believe these are contaminants as they come up in every single sample. I will test with a negative control in my next run to confirm, but I wanted to know if anyone else here is seeing the same.

From my research, I have seen that the RT enzyme used in scriptseq protocol is purified from Avian Myeloblastosis Virions, whose genomic material is probably still lurking around despite their purification attempts, so am guessing that these are contributing to the observed AMV reads. What I can't get around is where Bacillus sp reads are coming from. I clean my workstation 2X/ day. I wipe down everything and work under a hood. I also just wound up several RNAseq runs from vectors using a different protocol that utilizes NexteraXT indexes with the same machine, but I don't get the same issues with this.

dr_grm is offline   Reply With Quote

illumina, miseq, rnaseq, scriptseq

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