[cowsandmilk]

What other controls do you expect to see? Dataset S1 seems complete to me. There is a similar background level of indels both at the CXCR4 site and off-target 1 and off-target 2 sites. The experiment increases indels at the CXCR4 site, but not at the off-target sites.

[nonbel]

The proportion of HDR (ie HindIII reads only) without the template. What percent of cells will randomly mutate to get HindIII recognition sites?

Also, seeing what happens using template only would be good. We would expect low baseline levels of HDR to occur right? I it is plausible few out of 10^5 or 10^6 cells will require repair at that locus even without any Cas9.