Table 2 ∣.

Troubleshooting table

Step	Problem	Possible reason	Solution
63	No PCR products (Fig. 2e)	Initial cell sorting was not carried out properly	Ensure that cell sorting is handled properly
	>25 PCR cycles required and very pronounced satellite DNA bands visible	Bisulfite-converted DNA was degraded	Clean up the bisulfite-converted DNA immediately and perform the PCR amplification as quickly as possible. Keep bisulfite-converted DNA on ice when setting up the PCR reaction or put it in a −20 °C freezer directly if not PCR-amplifying right away
70	No PCR products (Fig. 2e)	Initial cell sorting was not carried out properly	Ensure that cell sorting is handled properly
	<2 ng of amplified cDNA	PCR cycle numbers were not optimized for the cell type	Increase the PCR cycle number up to 22 without jeopardizing mRNA representation
		The biotinylated RT-oligo–coated M-280 beads did not adequately bind mRNAs	Confirm that the biotinylated RT-oligo–coated beads are resuspended in the right buffer in Step 13
		Loss of M-280 beads, thereby bead-bound mRNAs, during washing	Make sure that no M-280 beads are improperly transferred to the plate containing gDNA from Steps 19–21
87	The sizes of RNA-seq library DNA are too large (>1,000 bp)	Too much cDNA added to tagmentation reaction	Reduce the cDNA concentration to 0.1 ng
90	No or very little (barely visible) RRBS library DNA (Fig. 2e)	Bisulfite-converted DNA was degraded between Steps 57 (purification of bisulfite-converted DNA) and 65 (RRBS library amplification)	Perform RRBS library amplification sooner rather than later and keep bisulfite-converted DNA frozen while performing Steps 59–63 (test PCR amplifications)