Table 1 |.

Troubleshooting table

Step	Problem	Possible reason	Solution
21	No DNA smear is present after PCR	Inadequate PCR amplification Failure of single-cell isolation DNA loss during processing the whole procedure	Perform three additional PCR cycles Prepare more single-cell libraries or repeat Sorting Repeat library preparation
	DNA smear with majority of molecular weight >300 bp	Under-digestion by MNase Over-amplification by PCR	Perform MNase titration Repeat library preparation and perform <25 PCR cycles
	Excessive adaptor dimer	Ratio of adaptor to insert DNA is too high	Reduce adaptor concentration
	DNA is present in no-MNase control	Apoptotic or dead cells	Exclude apoptotic or dead cells
30	<40% mappability of reads <0.5 million unique reads with redundancy >80%	Excessive adaptor dimer DNA loss during processing the whole procedure	Exclude dimer when excising bands from gel Repeat library preparation
	No enrichment of subnucleosome fragments at the TSS	Over-digestion by MNase Use of inactive TSS profile	Perform MNase titration Use expressed genes’ TSS profile
	No depletion of nucleosome fragments at the TSS	Under-digestion by MNase Use of inactive TSS profile	Perform MNase titration Use expressed genes’ TSS profile