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==Method== *Download human and mice reprogramming dataset *Merge genome-wide DNA methylation data of human and mice *Dendrogram based on genome-wide DNA methylation data(Figure 1a and 1b) *PCA analysis based on genome-wide DNA methylation data(Figure 2a and 2b) *heatmap based on DMR and DMRs in CpG Shore region (Figuare 1c,1d,1e and 1f) *1, cluster all scRNA by subset genes plu-diff *2, select good cells and separate ips and scnt *3, find differential express genes between ips and scnt *4, show previous knowledge base on this data *5, check Methylation to these DEG *6, find methylation biomarker/matric to show the difference between ips and scnt wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027571/suppl/GSM1027571_DNA_CpG_coverage_E14_serum_LIF.bedGraph.gz & wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027571/suppl/GSM1027571_DNA_CpG_methcounts_E14_serum_LIF.bedGraph.gz & wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027572/suppl/GSM1027572_DNA_CpG_coverage_E14_2i_adapted.bedGraph.gz & wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1027nnn/GSM1027572/suppl/GSM1027572_DNA_CpG_methcounts_E14_2i_adapted.bedGraph.gz & wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1127nnn/GSM1127953/suppl/GSM1127953_DNA_CpG_E14_serum_rep.bedGraph.gz & wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1127nnn/GSM1127954/suppl/GSM1127954_DNA_CpG_E14_2i_adapted_rep.bedGraph.gz &
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