Supplemental Files for publication "Cis-regulation and natural selection in the evolution of human DNA methylation"

Supplemental Files for publication "Cis-regulation and natural selection in the evolution of human DNA methylation" S1_regulation_CpG_sites (Referred to in the main text and supplemental figures as Supplemental File 1): csv files containing per-CpG site regulatory classification of DA, CNCC, IPSC, HEP, SKM using beta-binomial framework. Each row corresponds to a single CpG site, with columns indicating its genomic position, allele-specific methylation differences in parental and hybrid samples, statistical significance of cis and trans effects, and the resulting regulatory category (pure_cis, pure_trans, cis_plus_trans, cis_x_trans, or conserved). S1_coverage_information.txt: A text file containing coverage information of sequenced libraries, before and after allele-specific read phasing. The file includes per-sample coverage summary, post-bismark SNPsplit Phasing summary, post-phasing per-sample unique CpG positions, post-phasing unique CpG positions summary per cell type, a union/intersection summary of post-phasing unique CpG sites across samples in each cell type and assay (RRBS and WGBS). S1 variance partitioning analysis and regulatory site counts are uploaded as "01_02_betabinomial_regulation_classification (fig 1 2)/Supplemental_File_1_variance_explained_PVE_analysis.txt" at https://github.com/zhenzhenma120/The-causes-and-consequences-of-human-specific-DNA-methylation/tree/3281a617808949480ca063236bc2a83b7124bdae/01_02_betabinomial_regulation_classification%20(fig%201%202). S2_regulation_promoters (Referred to in the main text and supplemental figures as Supplemental File 2): csv files containing per-promoter regulatory classification of DA, CNCC, IPSC, HEP, SKM. Each row corresponds to a promoter region, with columns indicating its genomic position, allele-specific methylation differences in parental and hybrid samples, statistical significance of cis and trans effects, and the resulting regulatory category (pure_cis, pure_trans, cis_plus_trans, cis_x_trans, or conserved). S3_regulation_DMRs (Referred to in the main text and supplemental figures as Supplemental File 3): csv file containing de novo DMRs identified using changepoint detection and results from S1. Each row corresponds to a DMR, with columns indicating its genomic position, allele-specific methylation differences in parental and hybrid samples, statistical significance of cis and trans effects, and the resulting regulatory category (pure_cis, pure_trans, cis_plus_trans, cis_x_trans, or conserved). S4_transDMR_motifs (Referred to in the main text and supplemental figures as Supplemental File 4): Motif analysis results using de novo trans-DMRs identified from S3. Fold enrichment, p-values and Benjamini-Hochberg corrected q-values are reported in Hu>Ch and Hu