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==mouse public datasets to be used== *trans-differentiation GSE68601: WGBS "Frequent and Transient Acquisition of Pluripotency During Somatic Cell Trans-Differentiation with iPSCs Reprogramming Factors" GSM1676715 Whole Genome Bisulfite Sequencing from Mouse Embryonic Fibroblasts GSM1676716 Whole Genome Bisulfite Sequencing from from day 6 of OSKM trans-differentiation to Neural Stem Cells GSM1676717 Whole Genome Bisulfite Sequencing from from day 9 of OSKM trans-differentiation to Neural Stem Cells GSM1676718 Whole Genome Bisulfite Sequencing from v6.5 embryonic stem cells *mESC-serum GSE30206: Methylation profiling by high throughput sequencing "DNA-binding factors shape the mouse methylome at distal regulatory regions" GSM748786 MouseES_BisSeq_HiSeq GSM748787 MouseES_BisSeq_GAIIx GSE41923: WGBS "Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells" GSE61457: Methylation profiling by high throughput sequencing "Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells" GSM1505240 WT GSE68642: single cell WGBS "Parallel single-cell bisulfite sequencing link transcriptional and epigenetic heterogeneity" GSE56879: single cell WGBS "Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity" *mESC-2i NOT PUBLISHED - GSE59696: WGBS "The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors" GSE41923: WGBS "Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells" GSE68642: single cell WGBS "Parallel single-cell bisulfite sequencing link transcriptional and epigenetic heterogeneity" GSE56879: single cell WGBS "Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity" GSE70724: WGBS "Impairment of DNA methylation maintenance is the main cause of global demethylation in naïve ES cells" GSM1816835 E14_serum_To_2i_VitC_8h_H6A_WGBS GSM1816836 E14_serum_To_2i_VitC_4h_H5B_WGBS GSM1816837 E14_serum_To_2i_32h_H4A_WGBS GSM1816838 E14_serum_To_2i_4h_H1A_WGBS GSM1816839 E14_serum_To_2i_8h_H2A_WGBS GSM1816840 E14_serum_To_2i_VitC_32h_H8B_WGBS GSE71592: WGBS "An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cells" GSM1841059 WGBS_J1_2iVitC *other mouse samples GSE58610: MEF - WGBS "Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation" GSM1415152 MEF_WT1_1 GSM1415153 MEF_WT1_2 GSM1626094 MEF_WT2_1 GSE42836: multiple mouse primary tissue - WGBS "Tissue-specific methylomes reveal epigenetic memory in adult mouse tissue" GSE57527: colon epithelial - Methylation profiling by high throughput sequencing "Altered epigenetic programming links intestinal inflammation to colon cancer" GSE52330: dentate gyrus- Methylation profiling by high throughput sequencing "Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain" GSE47815: primary Hematopoietic Stem Cells - WGBS "Epigenetic and genetic changes during mouse hematopoietic stem cell aging " *additional sets GSE75408: Methylation profiling by high throughput sequencing "genomic DNA from MEF cells" (data not published) GSM1954518 WT GSM1954519 WT Dox GSE63417: zygote - WGBS (mice had genetic modification) "Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation" GSE72177: mouse liver - WGBS "Genetic and epigenetic variation among inbred littermates: identification of metastable epialleles in the mouse" GSE63568: EpiSCs - WGBS "An alternative pluripotent state confers interspecies chimaeric competency" GSE63330: placentas - Methylation profiling by high throughput sequencing "DNA methylation in mammalian placentas"
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