Retrospective analysis of enhancer activity and transcriptome history
) were also reanalyzed and plotted on the enhancer DMRs and the TSS of significantly labeled genes for each peak day separately.
The closest gene for each candidate enhancer was selected using BEDTools version 2.29.2. For both enhancers and their closest genes, we selected the day with the highest average TPM-normalized DCM count as peak day. The average TPM-normalized DCM counts per day were converted to z-scores for each region separately to visualize their patterns over time in heat maps. The density of enhancers per peak day in the 20-kb region around the genes per peak day was plotted using deepTools version 3.5.
Peaks were classified as labeled when at least one significant DCM site was overlapping the peak, whereas non-labeled peaks contained no significant DCM site. A set of random controls was generated by randomly permuting the H3K27ac peaks 100 times separately using BEDTools shuffle . The distance to the closest significant DCM site was plotted, and the number of overlapping DCM sites was counted.
The unique molecular identifier barcodes from each read were added to the read names using UMI-tools version 1.1.2 extract
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