Table 1. Carry-over E. coli DNA correlates closely with the heterologous spike-in for both fusion proteins and both low-salt/high-calcium and standard digestion conditions.

CUT&RUN was performed for H3K27me3 in parallel for pA/MNase Batch #6 (pA), pAG/MNase (pAG) using both low-salt/high-calcium (lo-hi) and standard (std) CUT&RUN digestion conditions. Each sample started with ~700,000 cells and 10 µL of bead slurry. Also varied in this experiment was addition of antibody followed by bead addition (Ab first) and addition of 0.1% BSA in the antibody buffer (BSA). Adding antibody first led to increased recovery of both yeast and E. coli DNA relative to human DNA, indicative of loss of cells prior to addition of fusion protein, possibly caused by loss of digitonin solubilization of membrane sugars.

H3K27me3	Ab first	BSA	Human	Yeast	E. coli	Corr (Sc:Ec)
pA lo-hi			5913983	743	3455	0.92
pA lo-hi		+	7748003	858	4988
pA lo-hi	+		5202278	2288	16110
pA lo-hi	+	+	5178086	1804	18759
pA std			6013347	595	2462	0.99
pA std		+	6005080	859	2295
pA std	+		4104736	2624	21236
pA std	+	+	3972820	2328	19245
pAG lo-hi			6999802	789	404	0.94
pAG lo-hi		+	6374939	642	467
pAG lo-hi	+		4140407	1565	1291
pAG lo-hi	+	+	4058693	2382	5289
pAG std			7514127	308	567	0.90
pAG std		+	5935592	355	125
pAG std	+		4594153	1271	555
pAG std	+	+	5379610	2509	1353