Mouse methylome studies SRP221485 Track Settings
 
Epigenetic regulator function through mouse gastrulation [Extraembryonic Ectoderm, proximal Epiblast]

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 SRX6836167  CpG methylation  proximal Epiblast / SRX6836167 (CpG methylation)   Schema 
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 SRX6836168  CpG methylation  Extraembryonic Ectoderm / SRX6836168 (CpG methylation)   Schema 
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 SRX6836169  HMR  proximal Epiblast / SRX6836169 (HMR)   Schema 
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 SRX6836169  CpG methylation  proximal Epiblast / SRX6836169 (CpG methylation)   Schema 
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 SRX6836171  HMR  SRS5377861 / SRX6836171 (HMR)   Schema 
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 SRX6836170  CpG methylation  Extraembryonic Ectoderm / SRX6836170 (CpG methylation)   Schema 
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 SRX6836173  HMR  SRS5377863 / SRX6836173 (HMR)   Schema 
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 SRX6836175  HMR  proximal Epiblast / SRX6836175 (HMR)   Schema 
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 SRX6836171  CpG methylation  SRS5377861 / SRX6836171 (CpG methylation)   Schema 
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 SRX6836177  HMR  proximal Epiblast / SRX6836177 (HMR)   Schema 
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 SRX6836172  CpG methylation  SRS5377862 / SRX6836172 (CpG methylation)   Schema 
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 SRX6836179  HMR  proximal Epiblast / SRX6836179 (HMR)   Schema 
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 SRX6836173  CpG methylation  SRS5377863 / SRX6836173 (CpG methylation)   Schema 
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 SRX6836181  HMR  proximal Epiblast / SRX6836181 (HMR)   Schema 
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 SRX6836174  CpG methylation  SRS5377864 / SRX6836174 (CpG methylation)   Schema 
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 SRX6836185  HMR  proximal Epiblast / SRX6836185 (HMR)   Schema 
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 SRX6836175  CpG methylation  proximal Epiblast / SRX6836175 (CpG methylation)   Schema 
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 SRX6836176  CpG methylation  Extraembryonic Ectoderm / SRX6836176 (CpG methylation)   Schema 
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 SRX6836186  HMR  proximal Epiblast / SRX6836186 (HMR)   Schema 
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 SRX6836177  CpG methylation  proximal Epiblast / SRX6836177 (CpG methylation)   Schema 
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 SRX6836189  HMR  proximal Epiblast / SRX6836189 (HMR)   Schema 
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 SRX6836202  HMR  proximal Epiblast / SRX6836202 (HMR)   Schema 
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 SRX6836178  CpG methylation  Extraembryonic Ectoderm / SRX6836178 (CpG methylation)   Schema 
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 SRX6836179  CpG methylation  proximal Epiblast / SRX6836179 (CpG methylation)   Schema 
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 SRX6836203  HMR  proximal Epiblast / SRX6836203 (HMR)   Schema 
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 SRX6836180  CpG methylation  Extraembryonic Ectoderm / SRX6836180 (CpG methylation)   Schema 
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 SRX7890100  HMR  proximal Epiblast / SRX7890100 (HMR)   Schema 
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 SRX6836181  CpG methylation  proximal Epiblast / SRX6836181 (CpG methylation)   Schema 
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 SRX6836182  CpG methylation  Extraembryonic Ectoderm / SRX6836182 (CpG methylation)   Schema 
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 SRX6836183  CpG methylation  Extraembryonic Ectoderm / SRX6836183 (CpG methylation)   Schema 
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 SRX6836184  CpG methylation  Extraembryonic Ectoderm / SRX6836184 (CpG methylation)   Schema 
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 SRX6836185  CpG methylation  proximal Epiblast / SRX6836185 (CpG methylation)   Schema 
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 SRX6836186  CpG methylation  proximal Epiblast / SRX6836186 (CpG methylation)   Schema 
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 SRX6836187  CpG methylation  Extraembryonic Ectoderm / SRX6836187 (CpG methylation)   Schema 
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 SRX6836188  CpG methylation  Extraembryonic Ectoderm / SRX6836188 (CpG methylation)   Schema 
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 SRX6836189  CpG methylation  proximal Epiblast / SRX6836189 (CpG methylation)   Schema 
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 SRX6836190  CpG methylation  Extraembryonic Ectoderm / SRX6836190 (CpG methylation)   Schema 
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 SRX6836202  CpG methylation  proximal Epiblast / SRX6836202 (CpG methylation)   Schema 
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 SRX6836203  CpG methylation  proximal Epiblast / SRX6836203 (CpG methylation)   Schema 
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 SRX7890098  CpG methylation  proximal Epiblast / SRX7890098 (CpG methylation)   Schema 
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 SRX7890099  CpG methylation  Extraembryonic Ectoderm / SRX7890099 (CpG methylation)   Schema 
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 SRX7890100  CpG methylation  proximal Epiblast / SRX7890100 (CpG methylation)   Schema 
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 SRX7890101  CpG methylation  Extraembryonic Ectoderm / SRX7890101 (CpG methylation)   Schema 
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 SRX7890102  CpG methylation  proximal Epiblast / SRX7890102 (CpG methylation)   Schema 
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 SRX7890103  CpG methylation  Extraembryonic Ectoderm / SRX7890103 (CpG methylation)   Schema 
    

Study title: Epigenetic regulator function through mouse gastrulation
SRA: SRP221485
GEO: GSE137337
Pubmed: 32728215

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX6836167 proximal Epiblast 0.729 22.6 37809 1097.5 463 1002.7 2515 8817.4 0.983 title: GSM4075629 BS-seq_KDM2B_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Kdm2b KO"}
SRX6836168 Extraembryonic Ectoderm 0.468 24.5 20733 16753.3 169 1036.4 1139 868618.0 0.987 title: GSM4075630 BS-seq_KDM2B_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Kdm2b KO"}
SRX6836169 proximal Epiblast 0.701 27.6 33529 1110.7 576 930.6 2200 8376.6 0.981 title: GSM4075631 BS-seq_L3MBTL2_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "L3mbtl2 KO"}
SRX6836170 Extraembryonic Ectoderm 0.441 22.5 16055 19822.8 133 1043.3 1250 785903.5 0.987 title: GSM4075632 BS-seq_L3MBTL2_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "L3mbtl2 KO"}
SRX6836171 SRS5377861 0.318 33.0 34292 1715.0 766 853.5 364 1313020.6 0.983 title: GSM4075633 BS-seq_DNMT1_E6.5_Epi, Mus musculus, Bisulfite-Seq; {}
SRX6836172 SRS5377862 0.143 27.9 5194 38571.8 35 819.9 1327 828502.0 0.988 title: GSM4075634 BS-seq_DNMT1_E6.5_ExE, Mus musculus, Bisulfite-Seq; {}
SRX6836173 SRS5377863 0.705 28.5 43713 1209.3 258 1156.7 3785 10826.6 0.984 title: GSM4075635 BS-seq_DNMT3A_E6.5_Epi, Mus musculus, Bisulfite-Seq; {}
SRX6836174 SRS5377864 0.407 23.8 15153 15797.7 90 1076.2 176 1823477.3 0.988 title: GSM4075636 BS-seq_DNMT3A_E6.5_ExE, Mus musculus, Bisulfite-Seq; {}
SRX6836175 proximal Epiblast 0.645 21.9 43309 1184.5 299 1004.6 3085 13552.6 0.987 title: GSM4075637 BS-seq_DNMT3B_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Dnmt3b KO"}
SRX6836176 Extraembryonic Ectoderm 0.299 19.6 13254 38023.8 231 977.0 3994 355930.6 0.989 title: GSM4075638 BS-seq_DNMT3B_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Dnmt3b KO"}
SRX6836177 proximal Epiblast 0.676 14.8 36027 1173.6 422 930.7 1830 9232.5 0.983 title: GSM4075639 BS-seq_G9A_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "G9a KO"}
SRX6836178 Extraembryonic Ectoderm 0.418 17.5 5443 51092.7 143 1060.2 2979 466819.6 0.987 title: GSM4075640 BS-seq_G9A_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "G9a KO"}
SRX6836179 proximal Epiblast 0.732 21.1 38692 1164.7 399 1070.2 3427 8698.9 0.983 title: GSM4075641 BS-seq_KMT2A_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Kmt2a KO"}
SRX6836180 Extraembryonic Ectoderm 0.492 20.8 23282 15056.6 145 1124.2 895 901562.3 0.988 title: GSM4075642 BS-seq_KMT2A_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Kmt2a KO"}
SRX6836181 proximal Epiblast 0.737 29.0 42381 1148.3 334 1095.1 3436 11075.4 0.983 title: GSM4075643 BS-seq_KMT2B_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Kmt2b KO"}
SRX6836182 Extraembryonic Ectoderm 0.428 26.3 6826 38463.0 156 1109.8 1915 650140.5 0.987 title: GSM4075644 BS-seq_KMT2B_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Kmt2b KO"}
SRX6836183 Extraembryonic Ectoderm 0.463 25.2 16857 20120.7 123 1088.5 1385 815191.8 0.988 title: GSM4075621 BS-seq_WT_E6.5_ExE_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "wild-type"}
SRX6836184 Extraembryonic Ectoderm 0.486 34.0 23489 15659.9 154 1108.7 1265 793898.4 0.987 title: GSM4075622 BS-seq_WT_E6.5_ExE_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "wild-type"}
SRX6836185 proximal Epiblast 0.717 47.2 43704 1084.8 614 964.1 3318 8816.0 0.983 title: GSM4075623 BS-seq_EED_E6.5_Epi_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Eed KO"}
SRX6836186 proximal Epiblast 0.726 35.6 42206 1089.6 469 970.1 2468 9148.5 0.983 title: GSM4075624 BS-seq_EED_E6.5_Epi_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Eed KO"}
SRX6836187 Extraembryonic Ectoderm 0.475 27.0 42743 11725.7 182 1019.6 2203 476742.0 0.987 title: GSM4075625 BS-seq_EED_E6.5_ExE_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Eed KO"}
SRX6836188 Extraembryonic Ectoderm 0.458 29.7 42231 12822.6 171 1040.5 2279 479146.2 0.987 title: GSM4075626 BS-seq_EED_E6.5_ExE_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Eed KO"}
SRX6836189 proximal Epiblast 0.692 15.5 34771 1108.0 541 915.5 1871 8649.1 0.983 title: GSM4075627 BS-seq_RNF2_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Rnf2 KO"}
SRX6836190 Extraembryonic Ectoderm 0.445 26.7 25547 16077.6 140 1073.6 1757 601427.9 0.987 title: GSM4075628 BS-seq_RNF2_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Rnf2 KO"}
SRX6836202 proximal Epiblast 0.757 50.6 45719 1150.8 503 977.0 4098 9233.2 0.982 title: GSM4075619 BS-seq_WT_E6.5_Epi_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "wild-type"}
SRX6836203 proximal Epiblast 0.762 45.2 46451 1145.6 486 1045.3 3971 9669.0 0.983 title: GSM4075620 BS-seq_WT_E6.5_Epi_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "wild-type"}
SRX7890098 proximal Epiblast 0.285 30.0 34351 3365.2 89 741.4 34 1243851.2 0.978 title: GSM4405460 DNMT1_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Dnmt1 KO"}
SRX7890099 Extraembryonic Ectoderm 0.106 25.6 471 101897.4 1 1271.0 1304 923538.1 0.983 title: GSM4405461 DNMT1_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Dnmt1 KO"}
SRX7890100 proximal Epiblast 0.722 21.4 43878 1279.4 239 1101.0 4511 11769.0 0.980 title: GSM4405462 DNMT3A_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Dnmt3a KO"}
SRX7890101 Extraembryonic Ectoderm 0.413 18.4 11182 20446.5 79 1216.8 237 1606834.0 0.984 title: GSM4405463 DNMT3A_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Dnmt3a KO"}
SRX7890102 proximal Epiblast 0.240 23.0 4170 72941.2 567 905.3 278 835630.6 0.985 title: GSM4405464 DNMT3AB_E6.5_Epi, Mus musculus, Bisulfite-Seq; {"source_name": "proximal Epiblast", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "proximal Epiblast", "dev_stage": "E6.5", "genotype": "Dnmt3a + Dnmt3b DKO"}
SRX7890103 Extraembryonic Ectoderm 0.114 16.9 4 519123.8 705 893.6 56 1333337.1 0.985 title: GSM4405465 DNMT3AB_E6.5_ExE, Mus musculus, Bisulfite-Seq; {"source_name": "Extraembryonic Ectoderm", "strain": "B6D2F1 maternal strain crossed with B6D2F1 males", "tissue": "Extraembryonic Ectoderm", "dev_stage": "E6.5", "genotype": "Dnmt3a + Dnmt3b DKO"}

Methods

All analysis was done using a bisulfite sequnecing data analysis pipeline DNMTools developed in the Smith lab at USC.

Mapping reads from bisulfite sequencing: Bisulfite treated reads are mapped to the genomes with the abismal program. Input reads are filtered by their quality, and adapter sequences in the 3' end of reads are trimmed. This is done with cutadapt. Uniquely mapped reads with mismatches/indels below given threshold are retained. For pair-end reads, if the two mates overlap, the overlapping part of the mate with lower quality is discarded. After mapping, we use the format command in dnmtools to merge mates for paired-end reads. We use the dnmtools uniq command to randomly select one from multiple reads mapped exactly to the same location. Without random oligos as UMIs, this is our best indication of PCR duplicates.

Estimating methylation levels: After reads are mapped and filtered, the dnmtools counts command is used to obtain read coverage and estimate methylation levels at individual cytosine sites. We count the number of methylated reads (those containing a C) and the number of unmethylated reads (those containing a T) at each nucleotide in a mapped read that corresponds to a cytosine in the reference genome. The methylation level of that cytosine is estimated as the ratio of methylated to total reads covering that cytosine. For cytosines in the symmetric CpG sequence context, reads from the both strands are collapsed to give a single estimate. Very rarely do the levels differ between strands (typically only if there has been a substitution, as in a somatic mutation), and this approach gives a better estimate.

Bisulfite conversion rate: The bisulfite conversion rate for an experiment is estimated with the dnmtools bsrate command, which computes the fraction of successfully converted nucleotides in reads (those read out as Ts) among all nucleotides in the reads mapped that map over cytosines in the reference genome. This is done either using a spike-in (e.g., lambda), the mitochondrial DNA, or the nuclear genome. In the latter case, only non-CpG sites are used. While this latter approach can be impacted by non-CpG cytosine methylation, in practice it never amounts to much.

Identifying hypomethylated regions (HMRs): In most mammalian cells, the majority of the genome has high methylation, and regions of low methylation are typically the interesting features. (This seems to be true for essentially all healthy differentiated cell types, but not cells of very early embryogenesis, various germ cells and precursors, and placental lineage cells.) These are valleys of low methylation are called hypomethylated regions (HMR) for historical reasons. To identify the HMRs, we use the dnmtools hmr command, which uses a statistical model that accounts for both the methylation level fluctations and the varying amounts of data available at each CpG site.

Partially methylated domains: Partially methylated domains are large genomic regions showing partial methylation observed in immortalized cell lines and cancerous cells. The pmd program is used to identify PMDs.

Allele-specific methylation: Allele-Specific methylated regions refers to regions where the parental allele is differentially methylated compared to the maternal allele. The program allelic is used to compute allele-specific methylation score can be computed for each CpG site by testing the linkage between methylation status of adjacent reads, and the program amrfinder is used to identify regions with allele-specific methylation.

For more detailed description of the methods of each step, please refer to the DNMTools documentation.