Sequencing problems of bacterial strains wihch produce a lot of EPS

[limno]

Hi,

I extracted the DNA by Chloroform extraction and had also a very high yield. But unfortunately as I started sequencing with the PacBio platform I had a veryy low number of reads. I assume that some organic molecules interfere with the polymerase. My bacterial strain is a strong EPS Producer and this is maybe the cause for the low read numbers.

Does anybody have any experience whith such Problems? Or can recommend me a protocol where I certainly get rid of all the EPS?

Thanks a lot...

Limno

[piyo2]

On PacBio's Sample Net, there is a shared protocol for using magnetic beads to remove contaminants. http://www.smrtcommunity.com/Share/P...eName=Protocol

I also advise contacting the local PacBio field applications scientist (yes, there is one in Switzerland). He may have some other tips on how to remove specific contaminants depending on the extraction and/or cleanup protocol you used.