Mouse methylome studies ERP008742 Track Settings
 
Germ_cell_methylation_dynamics [308-D5 TE Embryo 1, 308-D5 TE Embryo 2, 693-D6 TE Embryo 2, A3 mPGCLC1, BS treated DNA PBAT library, C3 mPGCLC2, D2 mPGCLC1, D3 mPGCLC2, E3 mPGCLC2, ESC, F1 hPGCLC1, F2 mPGCLC1, F3 mPGCLC2, G2 mPGCLC1, G3 mPGCLC2, H3 mPGCLC2, P11(4), P14(2), P8(3), PRGp8 4, Passage 10 Sort 2, Passage 10 Sort 3, Passage 10 Sort 4, S6EOSKSR 1, S6EOSKSR 3, S6EOSp15 1, S6EOSp15 2, S6EOSp5 3, S6EOSp9 1, S6EOSp9 2, S6EOSp9 3, hES1, hES2, hES3, hEpiLC 2016214 2, hEpiLC 201635, hKSR2, hKSR3, mEpiLC E14 d1 1, mEpiLC E14 d2 2]

Track collection: Mouse methylome studies

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experiment
ERX1048297 
ERX1048298 
ERX1048301 
ERX1048302 
ERX1048305 
ERX1048306 
ERX1048309 
ERX1048310 
ERX1265809 
ERX1265810 
ERX1265811 
ERX1265812 
ERX1265813 
ERX1265814 
ERX1265825 
ERX1265827 
ERX1265828 
ERX1265833 
ERX1265835 
ERX1265836 
ERX1265838 
ERX1265840 
ERX1265841 
ERX1265842 
ERX1265843 
ERX1265844 
ERX1265845 
ERX1275777 
ERX1275778 
ERX1275781 
ERX1275782 
ERX1275785 
ERX1275786 
ERX1275789 
ERX1275790 
ERX1709195 
ERX1709198 
ERX910723 
ERX910725 
ERX910726 
experiment
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 ERX1265838  HMR  A3 mPGCLC1 / ERX1265838 (HMR)   Schema 
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 ERX1048297  CpG methylation  ESC / ERX1048297 (CpG methylation)   Schema 
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 ERX910723  HMR  BS treated DNA PBAT library / ERX910723 (HMR)   Schema 
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 ERX1048298  CpG methylation  ESC / ERX1048298 (CpG methylation)   Schema 
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 ERX910725  HMR  BS treated DNA PBAT library / ERX910725 (HMR)   Schema 
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 ERX1048301  CpG methylation  ESC / ERX1048301 (CpG methylation)   Schema 
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 ERX910726  HMR  BS treated DNA PBAT library / ERX910726 (HMR)   Schema 
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 ERX1048302  CpG methylation  ESC / ERX1048302 (CpG methylation)   Schema 
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 ERX1048305  CpG methylation  ESC / ERX1048305 (CpG methylation)   Schema 
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 ERX1048306  CpG methylation  ESC / ERX1048306 (CpG methylation)   Schema 
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 ERX1048309  CpG methylation  ESC / ERX1048309 (CpG methylation)   Schema 
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 ERX1048310  CpG methylation  ESC / ERX1048310 (CpG methylation)   Schema 
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 ERX1265809  CpG methylation  C3 mPGCLC2 / ERX1265809 (CpG methylation)   Schema 
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 ERX1265810  CpG methylation  D3 mPGCLC2 / ERX1265810 (CpG methylation)   Schema 
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 ERX1265811  CpG methylation  E3 mPGCLC2 / ERX1265811 (CpG methylation)   Schema 
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 ERX1265812  CpG methylation  F3 mPGCLC2 / ERX1265812 (CpG methylation)   Schema 
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 ERX1265813  CpG methylation  G3 mPGCLC2 / ERX1265813 (CpG methylation)   Schema 
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 ERX1265814  CpG methylation  H3 mPGCLC2 / ERX1265814 (CpG methylation)   Schema 
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 ERX1265825  CpG methylation  D2 mPGCLC1 / ERX1265825 (CpG methylation)   Schema 
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 ERX1265827  CpG methylation  F2 mPGCLC1 / ERX1265827 (CpG methylation)   Schema 
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 ERX1265828  CpG methylation  G2 mPGCLC1 / ERX1265828 (CpG methylation)   Schema 
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 ERX1265833  CpG methylation  D2 mPGCLC1 / ERX1265833 (CpG methylation)   Schema 
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 ERX1265835  CpG methylation  F2 mPGCLC1 / ERX1265835 (CpG methylation)   Schema 
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 ERX1265836  CpG methylation  G2 mPGCLC1 / ERX1265836 (CpG methylation)   Schema 
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 ERX1265838  CpG methylation  A3 mPGCLC1 / ERX1265838 (CpG methylation)   Schema 
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 ERX1265840  CpG methylation  C3 mPGCLC2 / ERX1265840 (CpG methylation)   Schema 
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 ERX1265841  CpG methylation  D3 mPGCLC2 / ERX1265841 (CpG methylation)   Schema 
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 ERX1265842  CpG methylation  E3 mPGCLC2 / ERX1265842 (CpG methylation)   Schema 
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 ERX1265843  CpG methylation  F3 mPGCLC2 / ERX1265843 (CpG methylation)   Schema 
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 ERX1265844  CpG methylation  G3 mPGCLC2 / ERX1265844 (CpG methylation)   Schema 
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 ERX1265845  CpG methylation  H3 mPGCLC2 / ERX1265845 (CpG methylation)   Schema 
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 ERX1275777  CpG methylation  ESC / ERX1275777 (CpG methylation)   Schema 
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 ERX1275778  CpG methylation  ESC / ERX1275778 (CpG methylation)   Schema 
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 ERX1275781  CpG methylation  ESC / ERX1275781 (CpG methylation)   Schema 
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 ERX1275782  CpG methylation  ESC / ERX1275782 (CpG methylation)   Schema 
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 ERX1275785  CpG methylation  ESC / ERX1275785 (CpG methylation)   Schema 
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 ERX1275786  CpG methylation  ESC / ERX1275786 (CpG methylation)   Schema 
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 ERX1275789  CpG methylation  ESC / ERX1275789 (CpG methylation)   Schema 
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 ERX1275790  CpG methylation  ESC / ERX1275790 (CpG methylation)   Schema 
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 ERX1709195  CpG methylation  mEpiLC E14 d1 1 / ERX1709195 (CpG methylation)   Schema 
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 ERX1709198  CpG methylation  mEpiLC E14 d2 2 / ERX1709198 (CpG methylation)   Schema 
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 ERX910723  CpG methylation  BS treated DNA PBAT library / ERX910723 (CpG methylation)   Schema 
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 ERX910725  CpG methylation  BS treated DNA PBAT library / ERX910725 (CpG methylation)   Schema 
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 ERX910726  CpG methylation  BS treated DNA PBAT library / ERX910726 (CpG methylation)   Schema 
    

Study title: Germ_cell_methylation_dynamics
SRA: ERP008742
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
ERX1048297 ESC 0.368 3.1 1 796219.0 29 966.7 24 5973792.0 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:12:24Z", "External_Id": "SAMEA3335393", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:12:24Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S1-sc-2268397", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S1-sc-2268397", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1048298 ESC 0.394 3.4 582 25025.2 33 1035.2 59 4327364.1 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:05:53Z", "External_Id": "SAMEA3335394", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:05:53Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S2-sc-2268398", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S2-sc-2268398", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1048301 ESC 0.362 2.5 1 794408.0 38 953.2 20 7257956.9 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:06:25Z", "External_Id": "SAMEA3335397", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:06:25Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S5-sc-2268401", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S5-sc-2268401", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1048302 ESC 0.348 2.9 1 838820.0 17 980.4 30 6356506.1 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:14:18Z", "External_Id": "SAMEA3335398", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:14:18Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S6-sc-2268402", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S6-sc-2268402", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1048305 ESC 0.368 3.1 1 838820.0 38 1014.8 36 5469175.6 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:12:24Z", "External_Id": "SAMEA3335393", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:12:24Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S1-sc-2268397", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S1-sc-2268397", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1048306 ESC 0.394 3.4 435 27798.7 35 946.2 64 4361963.4 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:05:53Z", "External_Id": "SAMEA3335394", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:05:53Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S2-sc-2268398", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S2-sc-2268398", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1048309 ESC 0.362 2.5 1 795055.0 31 986.0 15 7820765.5 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:06:25Z", "External_Id": "SAMEA3335397", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:06:25Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S5-sc-2268401", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S5-sc-2268401", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1048310 ESC 0.348 2.9 2 765932.0 21 940.0 10 8593345.0 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:14:18Z", "External_Id": "SAMEA3335398", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:14:18Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S6-sc-2268402", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S6-sc-2268402", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265809 C3 mPGCLC2 0.196 2.0 1 657890.0 3 973.7 1 191994925.0 0.983 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:30Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:22Z", "External_Id": "SAMEA3512705", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:30Z", "INSDC_last_update": "2018-03-09T03:17:22Z", "INSDC_status": "public", "Submitter_Id": "C3_mPGCLC2-sc-2383195", "common_name": "house mouse", "description": "C3_mPGCLC2", "sample_name": "C3_mPGCLC2-sc-2383195", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265810 D3 mPGCLC2 0.217 2.1 2 634918.0 0 0.0 0 0.0 0.983 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512706", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "D3_mPGCLC2-sc-2383196", "common_name": "house mouse", "description": "D3_mPGCLC2", "sample_name": "D3_mPGCLC2-sc-2383196", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265811 E3 mPGCLC2 0.364 2.0 1 471503.0 10 791.2 13 8040469.1 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:22Z", "External_Id": "SAMEA3512707", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:17:22Z", "INSDC_status": "public", "Submitter_Id": "E3_mPGCLC2-sc-2383197", "common_name": "house mouse", "description": "E3_mPGCLC2", "sample_name": "E3_mPGCLC2-sc-2383197", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265812 F3 mPGCLC2 0.324 2.1 2 539157.5 14 883.4 2 10998295.0 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512708", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "F3_mPGCLC2-sc-2383198", "common_name": "house mouse", "description": "F3_mPGCLC2", "sample_name": "F3_mPGCLC2-sc-2383198", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265813 G3 mPGCLC2 0.355 2.5 1 710610.0 7 775.7 50 5053423.4 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:30Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:23Z", "External_Id": "SAMEA3512709", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:30Z", "INSDC_last_update": "2018-03-09T03:17:23Z", "INSDC_status": "public", "Submitter_Id": "G3_mPGCLC2-sc-2383199", "common_name": "house mouse", "description": "G3_mPGCLC2", "sample_name": "G3_mPGCLC2-sc-2383199", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265814 H3 mPGCLC2 0.400 2.3 8 116102.8 9 1077.9 153 681179.5 0.977 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:23Z", "External_Id": "SAMEA3512710", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:17:23Z", "INSDC_status": "public", "Submitter_Id": "H3_mPGCLC2-sc-2383200", "common_name": "house mouse", "description": "H3_mPGCLC2", "sample_name": "H3_mPGCLC2-sc-2383200", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265825 D2 mPGCLC1 0.356 2.2 3 522923.3 25 831.0 55 5037860.9 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512698", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "D2_mPGCLC1-sc-2383188", "common_name": "house mouse", "description": "D2_mPGCLC1", "sample_name": "D2_mPGCLC1-sc-2383188", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265827 F2 mPGCLC1 0.337 1.9 3 524415.3 17 799.7 22 7574648.0 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512700", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "F2_mPGCLC1-sc-2383190", "common_name": "house mouse", "description": "F2_mPGCLC1", "sample_name": "F2_mPGCLC1-sc-2383190", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265828 G2 mPGCLC1 0.310 1.9 1 490508.0 15 953.0 4 12428370.5 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:30Z", "ENA-LAST-UPDATE": "2018-03-09T03:38:15Z", "External_Id": "SAMEA3512701", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:30Z", "INSDC_last_update": "2018-03-09T03:38:15Z", "INSDC_status": "public", "Submitter_Id": "G2_mPGCLC1-sc-2383191", "common_name": "house mouse", "description": "G2_mPGCLC1", "sample_name": "G2_mPGCLC1-sc-2383191", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265833 D2 mPGCLC1 0.356 2.2 1 611522.0 23 903.4 33 5412641.2 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512698", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "D2_mPGCLC1-sc-2383188", "common_name": "house mouse", "description": "D2_mPGCLC1", "sample_name": "D2_mPGCLC1-sc-2383188", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265835 F2 mPGCLC1 0.337 1.9 1 462650.0 14 880.7 13 8045445.4 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512700", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "F2_mPGCLC1-sc-2383190", "common_name": "house mouse", "description": "F2_mPGCLC1", "sample_name": "F2_mPGCLC1-sc-2383190", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265836 G2 mPGCLC1 0.310 1.9 1 576749.0 11 855.6 1 13381157.0 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:30Z", "ENA-LAST-UPDATE": "2018-03-09T03:38:15Z", "External_Id": "SAMEA3512701", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:30Z", "INSDC_last_update": "2018-03-09T03:38:15Z", "INSDC_status": "public", "Submitter_Id": "G2_mPGCLC1-sc-2383191", "common_name": "house mouse", "description": "G2_mPGCLC1", "sample_name": "G2_mPGCLC1-sc-2383191", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265838 A3 mPGCLC1 0.642 2.0 27095 1662.7 20 863.0 366 121338.5 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:30Z", "ENA-LAST-UPDATE": "2018-03-09T04:30:19Z", "External_Id": "SAMEA3512703", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:30Z", "INSDC_last_update": "2018-03-09T04:30:19Z", "INSDC_status": "public", "Submitter_Id": "A3_mPGCLC1-sc-2383193", "common_name": "house mouse", "description": "A3_mPGCLC1", "sample_name": "A3_mPGCLC1-sc-2383193", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265840 C3 mPGCLC2 0.197 2.3 2 726912.5 4 945.0 0 0.0 0.984 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:30Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:22Z", "External_Id": "SAMEA3512705", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:30Z", "INSDC_last_update": "2018-03-09T03:17:22Z", "INSDC_status": "public", "Submitter_Id": "C3_mPGCLC2-sc-2383195", "common_name": "house mouse", "description": "C3_mPGCLC2", "sample_name": "C3_mPGCLC2-sc-2383195", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265841 D3 mPGCLC2 0.218 2.5 1 647677.0 1 636.0 0 0.0 0.983 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512706", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "D3_mPGCLC2-sc-2383196", "common_name": "house mouse", "description": "D3_mPGCLC2", "sample_name": "D3_mPGCLC2-sc-2383196", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265842 E3 mPGCLC2 0.365 2.3 1 796219.0 10 998.3 44 5150558.3 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:22Z", "External_Id": "SAMEA3512707", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:17:22Z", "INSDC_status": "public", "Submitter_Id": "E3_mPGCLC2-sc-2383197", "common_name": "house mouse", "description": "E3_mPGCLC2", "sample_name": "E3_mPGCLC2-sc-2383197", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265843 F3 mPGCLC2 0.325 2.4 1 838820.0 13 812.1 6 9648913.3 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:57:15Z", "External_Id": "SAMEA3512708", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:57:15Z", "INSDC_status": "public", "Submitter_Id": "F3_mPGCLC2-sc-2383198", "common_name": "house mouse", "description": "F3_mPGCLC2", "sample_name": "F3_mPGCLC2-sc-2383198", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265844 G3 mPGCLC2 0.356 2.8 1 796219.0 10 1139.1 58 4426827.7 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:30Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:23Z", "External_Id": "SAMEA3512709", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:30Z", "INSDC_last_update": "2018-03-09T03:17:23Z", "INSDC_status": "public", "Submitter_Id": "G3_mPGCLC2-sc-2383199", "common_name": "house mouse", "description": "G3_mPGCLC2", "sample_name": "G3_mPGCLC2-sc-2383199", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1265845 H3 mPGCLC2 0.401 2.6 232 42863.5 11 1223.7 327 379143.2 0.977 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-15T09:26:29Z", "ENA-LAST-UPDATE": "2018-03-09T03:17:23Z", "External_Id": "SAMEA3512710", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-15T09:26:29Z", "INSDC_last_update": "2018-03-09T03:17:23Z", "INSDC_status": "public", "Submitter_Id": "H3_mPGCLC2-sc-2383200", "common_name": "house mouse", "description": "H3_mPGCLC2", "sample_name": "H3_mPGCLC2-sc-2383200", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275777 ESC 0.367 3.1 2 901931.0 45 949.1 19 6464652.2 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:12:24Z", "External_Id": "SAMEA3335393", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:12:24Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S1-sc-2268397", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S1-sc-2268397", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275778 ESC 0.394 3.4 455 27139.3 33 911.5 70 4336838.6 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:05:53Z", "External_Id": "SAMEA3335394", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:05:53Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S2-sc-2268398", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S2-sc-2268398", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275781 ESC 0.361 2.5 1 795055.0 20 971.8 19 7015838.7 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:06:25Z", "External_Id": "SAMEA3335397", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:06:25Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S5-sc-2268401", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S5-sc-2268401", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275782 ESC 0.348 2.9 3 766662.0 18 1116.9 23 7059059.6 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:14:18Z", "External_Id": "SAMEA3335398", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:14:18Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S6-sc-2268402", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S6-sc-2268402", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275785 ESC 0.367 3.1 1 838820.0 45 939.4 22 6399575.4 0.979 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:12:24Z", "External_Id": "SAMEA3335393", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:12:24Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S1-sc-2268397", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S1-sc-2268397", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275786 ESC 0.394 3.4 722 23910.9 36 1089.0 79 4215825.6 0.982 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:05:53Z", "External_Id": "SAMEA3335394", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:05:53Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S2-sc-2268398", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S2-sc-2268398", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275789 ESC 0.361 2.5 1 743112.0 28 1035.9 9 8256100.6 0.978 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:06:25Z", "External_Id": "SAMEA3335397", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:06:25Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S5-sc-2268401", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S5-sc-2268401", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1275790 ESC 0.348 2.9 1 838820.0 14 1148.7 9 8830856.8 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"sex": "male", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-07-28T09:42:06Z", "ENA-LAST-UPDATE": "2018-03-09T00:14:18Z", "External_Id": "SAMEA3335398", "INSDC_center_name": "SC", "INSDC_first_public": "2015-07-28T09:42:06Z", "INSDC_last_update": "2018-03-09T00:14:18Z", "INSDC_status": "public", "Submitter_Id": "PBAT20150318_S6-sc-2268402", "common_name": "house mouse", "description": "PBAT libraries of mouse ESCs E14 G7", "sample_name": "PBAT20150318_S6-sc-2268402", "scientific_name": "Mus musculus", "strain": "E14"}
ERX1709195 mEpiLC E14 d1 1 0.266 4.1 1 1354581.0 5 949.4 0 0.0 0.997 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA_first_public": "2016-09-20", "ENA_last_update": "2016-05-20", "ENA-CHECKLIST": "ERC000011", "External_Id": "SAMEA3996570", "INSDC_center_alias": "SC", "INSDC_center_name": "Wellcome Sanger Institute", "INSDC_first_public": "2016-09-20T09:39:43Z", "INSDC_last_update": "2016-05-20T13:13:42Z", "INSDC_status": "public", "Submitter_Id": "83494700-1b75-11e6-b769-68b599768938", "common_name": "house mouse", "description": "mEpiLC_E14_d1_1", "sample_name": "83494700-1b75-11e6-b769-68b599768938", "strain": "E14"}
ERX1709198 mEpiLC E14 d2 2 0.496 2.8 24704 5126.4 2 1329.0 879 496619.7 0.994 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA_first_public": "2016-09-20", "ENA_last_update": "2016-05-20", "ENA-CHECKLIST": "ERC000011", "External_Id": "SAMEA3996572", "INSDC_center_alias": "SC", "INSDC_center_name": "Wellcome Sanger Institute", "INSDC_first_public": "2016-09-20T09:39:43Z", "INSDC_last_update": "2016-05-20T13:14:06Z", "INSDC_status": "public", "Submitter_Id": "835db960-1b75-11e6-b769-68b599768938", "common_name": "house mouse", "description": "mEpiLC_E14_d2_2", "sample_name": "835db960-1b75-11e6-b769-68b599768938", "strain": "E14"}
ERX910723 BS treated DNA PBAT library 0.647 1.9 22806 1751.5 5 980.0 96 100501.2 0.981 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-03-24T12:25:01Z", "ENA-LAST-UPDATE": "2018-03-08T22:17:52Z", "External_Id": "SAMEA3137578", "INSDC_center_name": "SC", "INSDC_first_public": "2015-03-24T12:25:01Z", "INSDC_last_update": "2018-03-08T22:17:52Z", "INSDC_status": "public", "Submitter_Id": "9_EB1_BS_sc-2176522", "common_name": "house mouse", "description": "BS treated DNA; PBAT library", "sample_name": "9_EB1_BS_sc-2176522", "scientific_name": "Mus musculus"}
ERX910725 BS treated DNA PBAT library 0.723 2.1 24882 1463.4 6 890.0 208 69545.7 0.979 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-03-24T12:25:01Z", "ENA-LAST-UPDATE": "2018-03-08T21:50:08Z", "External_Id": "SAMEA3137584", "INSDC_center_name": "SC", "INSDC_first_public": "2015-03-24T12:25:01Z", "INSDC_last_update": "2018-03-08T21:50:08Z", "INSDC_status": "public", "Submitter_Id": "11_EB2_B_sc-2176524", "common_name": "house mouse", "description": "BS treated DNA; PBAT library", "sample_name": "11_EB2_B_sc-2176524", "scientific_name": "Mus musculus"}
ERX910726 BS treated DNA PBAT library 0.658 1.7 22709 1709.4 7 999.6 165 85562.5 0.980 title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-03-24T12:25:01Z", "ENA-LAST-UPDATE": "2018-03-08T22:17:52Z", "External_Id": "SAMEA3137585", "INSDC_center_name": "SC", "INSDC_first_public": "2015-03-24T12:25:01Z", "INSDC_last_update": "2018-03-08T22:17:52Z", "INSDC_status": "public", "Submitter_Id": "12_EB2_BS_sc-2176525", "common_name": "house mouse", "description": "BS treated DNA; PBAT library", "sample_name": "12_EB2_BS_sc-2176525", "scientific_name": "Mus musculus"}

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.