Mouse methylome studies SRP219391 Track Settings
 
Maternal exposure to a mitochondrial toxicant results in life-long alterations in DNA methylation and gene expression in the offspring [Liver]

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 SRX6762232  CpG methylation  Liver / SRX6762232 (CpG methylation)   Schema 
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 SRX6762233  CpG methylation  Liver / SRX6762233 (CpG methylation)   Schema 
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 SRX6762235  HMR  Liver / SRX6762235 (HMR)   Schema 
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 SRX6762235  CpG methylation  Liver / SRX6762235 (CpG methylation)   Schema 
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 SRX6762236  CpG methylation  Liver / SRX6762236 (CpG methylation)   Schema 
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 SRX6762237  CpG methylation  Liver / SRX6762237 (CpG methylation)   Schema 
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 SRX6762238  CpG methylation  Liver / SRX6762238 (CpG methylation)   Schema 
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 SRX6762239  CpG methylation  Liver / SRX6762239 (CpG methylation)   Schema 
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 SRX6762240  HMR  Liver / SRX6762240 (HMR)   Schema 
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 SRX6762240  CpG methylation  Liver / SRX6762240 (CpG methylation)   Schema 
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 SRX6762241  CpG methylation  Liver / SRX6762241 (CpG methylation)   Schema 
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 SRX6762242  HMR  Liver / SRX6762242 (HMR)   Schema 
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 SRX6762242  CpG methylation  Liver / SRX6762242 (CpG methylation)   Schema 
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 SRX6762243  HMR  Liver / SRX6762243 (HMR)   Schema 
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 SRX6762243  CpG methylation  Liver / SRX6762243 (CpG methylation)   Schema 
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 SRX6762244  HMR  Liver / SRX6762244 (HMR)   Schema 
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 SRX6762244  CpG methylation  Liver / SRX6762244 (CpG methylation)   Schema 
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 SRX6762245  CpG methylation  Liver / SRX6762245 (CpG methylation)   Schema 
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 SRX6762246  CpG methylation  Liver / SRX6762246 (CpG methylation)   Schema 
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 SRX6762247  CpG methylation  Liver / SRX6762247 (CpG methylation)   Schema 
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 SRX6762248  CpG methylation  Liver / SRX6762248 (CpG methylation)   Schema 
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 SRX6762249  HMR  Liver / SRX6762249 (HMR)   Schema 
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 SRX6762249  CpG methylation  Liver / SRX6762249 (CpG methylation)   Schema 
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 SRX6762250  CpG methylation  Liver / SRX6762250 (CpG methylation)   Schema 
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 SRX6762251  CpG methylation  Liver / SRX6762251 (CpG methylation)   Schema 
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 SRX6762252  CpG methylation  Liver / SRX6762252 (CpG methylation)   Schema 
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 SRX6762253  CpG methylation  Liver / SRX6762253 (CpG methylation)   Schema 
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 SRX6762254  CpG methylation  Liver / SRX6762254 (CpG methylation)   Schema 
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 SRX6762255  CpG methylation  Liver / SRX6762255 (CpG methylation)   Schema 
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 SRX6762256  CpG methylation  Liver / SRX6762256 (CpG methylation)   Schema 
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 SRX6762257  CpG methylation  Liver / SRX6762257 (CpG methylation)   Schema 
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 SRX6762258  CpG methylation  Liver / SRX6762258 (CpG methylation)   Schema 
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 SRX6762259  CpG methylation  Liver / SRX6762259 (CpG methylation)   Schema 
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 SRX6762260  CpG methylation  Liver / SRX6762260 (CpG methylation)   Schema 
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 SRX6762261  CpG methylation  Liver / SRX6762261 (CpG methylation)   Schema 
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 SRX6762262  HMR  Liver / SRX6762262 (HMR)   Schema 
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 SRX6762262  CpG methylation  Liver / SRX6762262 (CpG methylation)   Schema 
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 SRX6762263  HMR  Liver / SRX6762263 (HMR)   Schema 
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 SRX6762263  CpG methylation  Liver / SRX6762263 (CpG methylation)   Schema 
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 SRX6762264  HMR  Liver / SRX6762264 (HMR)   Schema 
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 SRX6762264  CpG methylation  Liver / SRX6762264 (CpG methylation)   Schema 
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 SRX6762265  HMR  Liver / SRX6762265 (HMR)   Schema 
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 SRX6762265  CpG methylation  Liver / SRX6762265 (CpG methylation)   Schema 
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 SRX6762266  HMR  Liver / SRX6762266 (HMR)   Schema 
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 SRX6762266  CpG methylation  Liver / SRX6762266 (CpG methylation)   Schema 
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 SRX6762267  HMR  Liver / SRX6762267 (HMR)   Schema 
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 SRX6762267  CpG methylation  Liver / SRX6762267 (CpG methylation)   Schema 
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 SRX6762268  HMR  Liver / SRX6762268 (HMR)   Schema 
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 SRX6762268  CpG methylation  Liver / SRX6762268 (CpG methylation)   Schema 
    

Study title: Maternal exposure to a mitochondrial toxicant results in life-long alterations in DNA methylation and gene expression in the offspring
SRA: SRP219391
GEO: GSE136417
Pubmed: 32937126

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX6762228 Liver 0.723 12.1 36411 1273.2 830 989.9 2162 8524.4 0.981 title: GSM4048730 D22-0ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "PND22", "dam_treatment": "control"}
SRX6762229 Liver 0.733 11.4 35450 1300.5 647 998.7 2207 8246.9 0.981 title: GSM4048731 D22-0ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "PND22", "dam_treatment": "control"}
SRX6762230 Liver 0.727 7.9 32504 1381.6 177 950.7 1050 11669.7 0.980 title: GSM4048732 D22-0ppm-female-rep4.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "PND22", "dam_treatment": "control"}
SRX6762231 Liver 0.719 9.5 34113 1344.3 811 1002.9 921 14055.9 0.982 title: GSM4048733 D22-10ppm-female-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "PND22", "dam_treatment": "10ppm rotenone"}
SRX6762232 Liver 0.713 10.3 34263 1341.7 609 955.8 2134 8284.7 0.981 title: GSM4048734 D22-10ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "PND22", "dam_treatment": "10ppm rotenone"}
SRX6762233 Liver 0.735 7.8 33093 1400.5 139 901.9 902 13011.1 0.980 title: GSM4048735 D22-10ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "PND22", "dam_treatment": "10ppm rotenone"}
SRX6762235 Liver 0.751 9.5 37863 1350.6 165 938.6 1499 12640.0 0.981 title: GSM4048737 6mo-0ppm-female-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "control"}
SRX6762236 Liver 0.709 9.8 34743 1390.0 2168 1210.8 1352 14417.3 0.981 title: GSM4048738 6mo-0ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "control"}
SRX6762237 Liver 0.704 4.3 23311 1925.6 1048 1247.5 527 25905.6 0.985 title: GSM4048739 6mo-0ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "control"}
SRX6762238 Liver 0.709 3.5 21962 1981.3 656 1230.1 485 28213.5 0.985 title: GSM4048740 6mo-0ppm-female-rep4.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "control"}
SRX6762239 Liver 0.749 9.2 35765 1403.2 160 883.0 1521 12400.1 0.981 title: GSM4048741 6mo-0ppm-female-rep5.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "control"}
SRX6762240 Liver 0.697 3.7 22422 1991.7 1082 1285.3 446 31977.7 0.984 title: GSM4048742 6mo-10ppm-female-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "10ppm rotenone"}
SRX6762241 Liver 0.693 4.5 23560 1926.5 1158 1241.5 427 28839.3 0.985 title: GSM4048743 6mo-10ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "10ppm rotenone"}
SRX6762242 Liver 0.752 9.6 38812 1358.2 185 968.9 1549 13280.3 0.980 title: GSM4048744 6mo-10ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "10ppm rotenone"}
SRX6762243 Liver 0.748 10.1 37530 1355.3 189 945.4 1557 11945.2 0.980 title: GSM4048745 6mo-10ppm-female-rep4.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "10ppm rotenone"}
SRX6762244 Liver 0.727 15.8 39732 1312.5 1110 981.6 2683 9168.2 0.982 title: GSM4048746 6mo-10ppm-female-rep5.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "6 months", "dam_treatment": "10ppm rotenone"}
SRX6762245 Liver 0.676 6.7 27207 1799.0 1676 1199.2 965 19380.2 0.982 title: GSM4048747 12mo-0ppm-female-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "12 months", "dam_treatment": "control"}
SRX6762246 Liver 0.710 9.3 30457 1636.8 1206 1080.7 1466 13684.0 0.983 title: GSM4048748 12mo-0ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "12 months", "dam_treatment": "control"}
SRX6762247 Liver 0.692 6.7 22191 1967.2 944 1094.4 776 20492.1 0.982 title: GSM4048749 12mo-0ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "12 months", "dam_treatment": "control"}
SRX6762248 Liver 0.700 9.4 31735 1660.3 1088 1086.1 1368 15062.0 0.982 title: GSM4048750 12mo-10ppm-female-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "12 months", "dam_treatment": "10ppm rotenone"}
SRX6762249 Liver 0.722 9.5 32453 1589.8 1532 1117.4 1385 14071.2 0.984 title: GSM4048751 12mo-10ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "12 months", "dam_treatment": "10ppm rotenone"}
SRX6762250 Liver 0.714 7.7 27420 1665.2 1478 1110.8 964 14610.3 0.984 title: GSM4048752 12mo-10ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "12 months", "dam_treatment": "10ppm rotenone"}
SRX6762251 Liver 0.723 10.3 31657 1610.8 2151 1128.6 1189 15228.2 0.983 title: GSM4048753 18mo-0ppm-female-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "18 months", "dam_treatment": "control"}
SRX6762252 Liver 0.726 10.6 32452 1567.7 1382 1078.2 1380 13725.5 0.984 title: GSM4048754 18mo-0ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "18 months", "dam_treatment": "control"}
SRX6762253 Liver 0.717 7.0 28278 1697.0 1644 1189.5 893 19454.2 0.984 title: GSM4048755 18mo-0ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "18 months", "dam_treatment": "control"}
SRX6762254 Liver 0.716 9.9 29117 1628.9 2310 1132.1 981 16693.3 0.984 title: GSM4048756 18mo-10ppm-female-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "18 months", "dam_treatment": "10ppm rotenone"}
SRX6762255 Liver 0.714 5.1 24270 1932.0 912 1243.3 576 27636.0 0.984 title: GSM4048757 18mo-10ppm-female-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "18 months", "dam_treatment": "10ppm rotenone"}
SRX6762256 Liver 0.703 4.8 25014 1877.4 735 1170.8 782 22023.9 0.984 title: GSM4048758 18mo-10ppm-female-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "female", "age": "18 months", "dam_treatment": "10ppm rotenone"}
SRX6762257 Liver 0.726 9.3 33884 1342.8 187 998.2 1107 12668.7 0.981 title: GSM4048759 D22-0ppm-male-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "PND22", "dam_treatment": "control"}
SRX6762258 Liver 0.730 9.0 33083 1365.9 182 977.0 1128 12305.2 0.981 title: GSM4048760 D22-0ppm-male-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "PND22", "dam_treatment": "control"}
SRX6762259 Liver 0.736 9.4 33624 1360.8 207 978.0 1201 12479.3 0.980 title: GSM4048761 D22-0ppm-male-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "PND22", "dam_treatment": "control"}
SRX6762260 Liver 0.745 6.8 33025 1408.4 155 987.6 969 15030.3 0.980 title: GSM4048762 D22-10ppm-male-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "PND22", "dam_treatment": "10ppm rotenone"}
SRX6762261 Liver 0.733 7.0 32478 1428.6 122 947.5 888 13648.0 0.980 title: GSM4048763 D22-10ppm-male-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "PND22", "dam_treatment": "10ppm rotenone"}
SRX6762262 Liver 0.730 7.6 31046 1411.9 150 930.2 935 13248.2 0.980 title: GSM4048764 D22-10ppm-male-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "PND22", "dam_treatment": "10ppm rotenone"}
SRX6762263 Liver 0.735 10.9 36801 1279.2 258 926.3 1289 12433.1 0.980 title: GSM4048765 6mo-0ppm-male-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "6 months", "dam_treatment": "control"}
SRX6762264 Liver 0.756 9.1 39370 1372.8 194 907.4 1680 13929.3 0.980 title: GSM4048766 6mo-0ppm-male-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "6 months", "dam_treatment": "control"}
SRX6762265 Liver 0.750 10.3 40843 1327.0 229 917.9 1631 14342.4 0.980 title: GSM4048767 6mo-0ppm-male-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "6 months", "dam_treatment": "control"}
SRX6762266 Liver 0.732 9.7 39619 1342.0 180 934.6 1358 13756.0 0.980 title: GSM4048768 6mo-10ppm-male-rep1.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "6 months", "dam_treatment": "10ppm rotenone"}
SRX6762267 Liver 0.739 10.4 39905 1320.9 241 924.9 1328 14535.6 0.980 title: GSM4048769 6mo-10ppm-male-rep2.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "6 months", "dam_treatment": "10ppm rotenone"}
SRX6762268 Liver 0.753 9.6 40120 1355.9 232 917.8 1427 15137.6 0.980 title: GSM4048770 6mo-10ppm-male-rep3.WGBS, Mus musculus, Bisulfite-Seq; {"source_name": "mouse liver", "tissue": "liver", "sex": "male", "age": "6 months", "dam_treatment": "10ppm rotenone"}

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.