Top 500 putative identity genes ranked by the CIG score are selected to perform the DAVID pathway analysis (DAVID 6.8 https://david.ncifcrf.gov/) ⁶. The pathways with significant q value <0.05 (Benjamini) were selected to make the bar plot by using excel (Fig 5A).

We used the Profile function in DANPOS version 2.2.3 to compare the 4 epigenetic profiles between putative identity genes and control genes around the promoter region (-3kb to 10kb of TSS):

python danpos.py profile wig --genefile_paths putative_identity_genes.txt,putative_negative_identity_genes.txt --genefile_aliases positive,negative --heatmap 1 --name outdir --genomic_sites TSS --flank_up 3000 --flank_dn 10000

CRISP9 gRNA and mutation primers design