Table 1. Embryonic DNA methylation datasets used in this study.
DKO, double knockout; E, gestational day; ESC, embryonic stem cell; ext ect, extraembryonic ectoderm; ext end, extraembryonic endoderm; GW, gestational weeks; iPSC, induced pluripotent stem cell; KO, knockout; P, passage; TKO, triple knockout; RRBS, reduced representation bisulfite sequencing; WGBS, whole-genome bisulfite sequencing; WT, wild type.
| Name | Reference | Accession | Platform | Species | Samples (number of biological replicates) |
| Dataset 1 | (63) | GSE34864 | RRBS | Mouse | Zygote (5), 2-cell (4), 4-cell (5), 8-cell (3), ICM (5), E6.5 (4), E7.5 (5) |
| Dataset 2 | (55) | GSE56697 | WGBS | Mouse | 2-cell (2), 4-cell (2), E3.5 (3), E6.5 (2), E7.5 (2), E13.5 (2) |
| Dataset 3 | (64) | GSE98151 | WGBS | Mouse | Zygote (1), early 2 cell (1), late 2 cell (1), 4 cell (1), 8 cell (1), morula (1), ICM (1), trophoblast (1), E6.5 epiblast (1), E6.5 ext ect (1), E7.5 epiblast (1), E7.5 ext ect (1) |
| Dataset 4 | (48) | GSE121690 | scNMT-seq | Mouse | 758 single cells from E4.5, E5.5, E6.5, E7.5 |
| Dataset 5 | (69) | GSE51239 | RRBS | Mouse | ICM (2), trophectoderm (2), E6.5 epiblast (2), E6.5 ext end (2), ESC P0–P5 (17) |
| Dataset 6 | (66) | ENCSR486XIX | WGBS | Mouse | Various tissues from E10.5 to birth (139) |
| Dataset 7 | (70) | GSE56515 | 450K array | Human | Various tissues from GW 9 to GW 22 (34) |
| Dataset 8 | (71) | GSE31848 | 450K array | Human | Various tissues from GW 14 to GW 20 (37) |
| Dataset 9 | (72) | GSE69502 | 450K array | Human | Various tissues from GW 14.5 to 23 (49) |
| Dataset 10 | (71) | GSE31848 | 450K array | Human | ESC P9–P105 (19), iPSC P5–P37 (29) |
| Dataset 11 | (73) | GSE34869 | 450K array | Human | ESC P32–P114 (19), iPSC P12–P21 (5) |
| Dataset 12 | (74) | GSE40909 | 450K array | Human | ESC P41–P49 (3), iPSC P6 (2) |
| Dataset 13 | (75) | GSE44424 | 27K array | Human | ESC P29–P87 (8), iPSC P9–P21 (21) |
| Dataset 14 | (76) | GSE51747 | 27K array | Human | ESC P52–P64 (3), iPSC P9–P17 (6) |
| Dataset 15 | (71) | GSE30653 | 27K array | Human | ESC P9–P114 (116), iPSC P4–P69 (46) |
| Dataset 16 | (77) | GSE54848 | 450K array | Human | iPSC P1–P3 (9) |
| Dataset 17 | (47) | GSE76261 | PBAT | Mouse | TET TKO (2) and WT E6.5 epiblast (2) |
| Dataset 18 | (48) | GSE133687 | scNMT-seq | Mouse | TET TKO (126) and WT ESCs (136) at days 2, 5, and 7 of differentiation |
| Dataset 19 | (51) | GSE130735 | RRBS | Mouse | KO of DNMT1 (3), DKO of DNMT3A/3B (6), WT (5), heterozygous control (6) |
| Dataset 20 | (46) | GSE60334 | RRBS | Mouse | E3.5-, E4.5 blastocyst (1-1), E5.5-, E6.5-, E7.5 epiblast (1-1-1), E8.5-, E10 whole embryos (3-2), E11.5 limbs (2) |