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===Results=== *total # of DMS between human SCNT and iPSC (hg19, Ma et al): 111 *Here are the # of DMRs we found that overlapped with different functional regions within the human genome (annotation downloaded from UCSC table browser): **CpG island: 7 (2bp DMS p-value: <10^-6) **CpG shore: 12 (2bp DMS p-value: 0.00063, fold of enrichment: 3.02 ) **CpG shelf: 10 (2bp DMS p-value: 0.00524 *total # of DMS between mouse SCNT (2 lines cultured with serum) and 4 iPSC lines: 489 (0.05 FDR) *Here are the # of DMRs we found that overlapped with different functional regions within the mouse genome (annotation downloaded from UCSC table browser): **CpG island: (2bp DMS p-value: ) **CpG shore: 28 (2bp DMS p-value: 5.214671e-05; fold of enrichment:) **CpG shelf: (2bp DMS P-value: ) **DNase I hypersensitive sites (UCSC ENCODE data from UW): ~88 (2bp DMS, p-value: <10^-6) **Enhancer for Oct4, Sox2, Nanog, Med1, H3K27Ac, Klf4, and Esrrb in mESC: 10 (2bp DMS, p-value: 0.00053) (reference: Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes. Whyte et al. Cell. 2013) **superenhancer and typical enhancer ChiP-Seq data: (reference: Super-Enhancers in the Control of Cell Identity and Disease, doi:10.1016/j.cell.2013.09.053) *total # of DMR we identified overlapped with topological domains that were previously published by Ren lab (source: Dixon JR et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376-380) **J1 mESC data (HindIII_combined,mm9) **total # of DMS overlapped with topological domains: 457 (2bp DMS, p-value: 0.013291)
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