BS-seq analyses
BS-seq libraries were obtained from the NCBI Sequence Read Archive (SRA). Quality control procedures for raw reads were conducted using FastQC v0.12.1 program. Reads with Q20 > 90% were retained for downstream analysis. Subsequent read mapping to the corresponding reference genome was performed using Bismark v0.24.2 (Krueger and Andrews, 2011) with default parameters. Read alignment within Bismark utilized Bowtie2 v2.3.5.1 (Langmead and Salzberg, 2012).

Krueger, F., and Andrews, S.R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572.
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359.