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Old 08-12-2014, 11:40 AM   #14
Junior Member
Location: Cambridge, MA

Join Date: Jan 2011
Posts: 3

hi ju,

cool to see that you have reduced mtDNA with changing lysis conditions. did you ever do a technical replicate with .01% and .1%? it would be nice to quantitate the background noise at different lysis conditions. i don't think mtDNA contamination per se would change your signal to noise ratio but the changing lysis conditions might.

as for primary cells, we have had some experience working with blood cell types and our results are generally similar to what the original ATAC-seq paper reported in T cells. so as far as we know, the protocol works just fine in primary cells.

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