Table 1 High throughput profiles of DNA methylation, histone modification, transcription and protein binding data sets analyzed in this study. ID represents accession identifiers of the datasets in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [45, 92] or the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) ArrayExpress [73, 93] databases, along with the reference publications. Target marks are the types of molecular targets represented in the datasets. Cell type notation: mouse embryonic stem cell (ESC), mouse embryonic fibroblast (MEF), wild type (WT), knockout (KO). Sequencing methods notation: Whole-Genome Bisulfite Sequencing (WGBS), Tet-Associated Bisulfite sequencing (TAB-seq), Reduced Representation Bisulfite Sequencing (RRBS), Chromatin Immunoprecipitation sequencing (ChIP-seq), RNA sequencing (RNA-seq)
Row | GEO ID | Target marks | Cell type/tissue | Method | Reference |
|---|---|---|---|---|---|
1 | GSE30206 | DNA methylation | ESC | WGBS | Stadler et al. [56] |
2 | GSE44760 | DNA methylation | MEF (WT, Dnmt1 KO) | RRBS | Reddington et al. [59] |
3 | GSE36173 | DNA hydroxymethylation | ESC | TAB-seq | Yu et al. [79] |
4 | GSE29218 | H3K4me1, H3K4me3, Pol2, CTCF, H3K27ac, P300 | ESC, MEF, Cortex, Liver | ChIP-seq | Shen et al. [45] |
5 | GSE12241 | H3, H4K20me3, H3K36me3, H3K9me3 | ESC, MEF | ChIP-seq | Mikkelsen et al. [38] |
6 | GSE28254 | H3K27me3 | ESC | ChIP-seq | Brinkman et al. [94] |
7 | GSE29413 | H3K9me3 | ESC | ChIP-seq | Karimi et al. [95] |
8 | E-ERAD-79 | H3K4me(1,3) | ESC (WT, Cfp1 KO) | ChIP-seq | Clouaire et al. [39] |
9 | GSE41440 | H3K4me1, H3K27me3 | MEF (WT, Mll1 KO) | ChIP-seq | Herz et al. [33] |
10 | GSE44393 | H3K4me3, H3K27me3 | MEF (WT, Dnmt1 KO) | ChIP-seq | Reddington et al. [59] |
11 | GSE39610 | MBD (1A,1B,2,3,4), MECP2 | ESC | ChIP-seq | Baubec et al. [16] |
12 | GSE34094 | CTCF | ESC | ChIP-seq | Sleutels et al. [96] |
13 | GSE37338 | Transcription | ESC | RNA-seq | Livyatan et al. [97] |
14 | GSE44733 | Transcription | MEF (WT, Dnmt1 KO) | RNA-seq | Reddington et al. [59] |
15 | GSE42836 | DNA methylation | Liver, Cortex | WGBS | Hon et al. [98] |