. Author manuscript; available in PMC: 2020 Jun 24.

Published in final edited form as: Nat Protoc. 2019 Oct 16;14(11):3243–3272. doi: 10.1038/s41596-019-0229-4

Table 3.

Empirical thresholds for quantitative evaluation of broken nuclei. These thresholds should be applied to the ratios of the measured amounts of sRNA and nRNA (sRNA/nDNA column) and the amounts of sDNA and nDNA (sDNA/nDNA column). The sRNA and sDNA should be obtained from the supernatant in Steps 23, 28, 32, 50, and 56 (rows). nRNA and nDNA should be obtained from Step 72. Any obtained ratio at any of these steps beyond the listed threshold of that step is a sign of having a non-negligible fraction of broken nuclei.

Step # for retrieving sRNA and sDNA	sRNA/nRNA	sDNA/nDNA
Step 23	10/100	1/100
Step 28	1/100	1/100
Step 32	1/100	1/100
Step 50	1/100	1/100
Step 56	1/100	1/100