Mouse methylome studies ERP003907 Track Settings
 
Methylome_and_Hydroxymethylome_of_iPSC [2769STDY6182410-sc-2382182, 2769STDY6182411-sc-2382183, BSeq_MEF1-sc-1861756, BSeq_MEF2-sc-1861757, BSeq_MEF3-sc-1861758, BSeq_P29_iPSC44-sc-2014730, BSeq_P29_iPSC45-sc-2014731, BSeq_P29_iPSC66-sc-2014732, BSeq_P29_iPSC67-sc-2014733, BSeq_P29_iPSC72-sc-2014734, BSeq_P29_iPSC73-sc-2014735, BSeq_P8_iPSC67-sc-1861783, BSeq_P8_iPSC73-sc-1861785, BSeq_TMBD1-sc-1861759, BSeq_TMBD2-sc-1861760, BSeq_TMBD3-sc-1861761, BSeq_T_S_Exp10-sc-1861768, BSeq_T_S_Exp10-sc-1861769, BSeq_T_S_Exp11-sc-1861770, BSeq_T_S_Exp11-sc-1861771, BSeq_T_S_Exp16-sc-1861772, BSeq_T_S_Exp16-sc-1861773, TMBD10_BS-sc-2013-09-18T12:28:21Z-1692906, TMBD10_oxBS-sc-2013-09-18T12:28:31Z-1692907, iPSC19_BS-sc-2013-09-18T12:30:10Z-1692914, iPSC19_oxBS-sc-2013-09-18T12:31:26Z-1692918, iPSC20_BS-sc-2013-09-18T12:31:06Z-1692915, iPSC20_oxBS-sc-2013-09-18T12:30:31Z-1692919, iPSC27_BS-sc-2013-09-18T12:28:40Z-1692908, iPSC27_oxBS-sc-2013-09-18T12:29:46Z-1692911, iPSC28_BS-sc-2013-09-18T12:30:17Z-1692909, iPSC28_oxBS-sc-2013-09-18T12:29:53Z-1692912, iPSC29_BS-sc-2013-09-18T12:30:24Z-1692910, iPSC29_oxBS-sc-2013-09-18T12:30:03Z-1692913, iPSC37_BS-sc-2013-09-18T12:31:14Z-1692916, iPSC37_oxBS-sc-2013-09-18T12:30:37Z-1692920, iPSC38_BS-sc-2013-09-18T12:31:20Z-1692917, iPSC38_oxBS-sc-2013-09-18T12:30:43Z-1692921, oxBSeq_MEF1-sc-1861762, oxBSeq_MEF2-sc-1861763, oxBSeq_MEF3-sc-1861764, oxBSeq_P29_iPSC44-sc-2014736, oxBSeq_P29_iPSC45-sc-2014737, oxBSeq_P29_iPSC66-sc-2014738, oxBSeq_P29_iPSC67-sc-2014739, oxBSeq_P29_iPSC72-sc-2014740, oxBSeq_P29_iPSC73-sc-2014741, oxBSeq_TMBD1-sc-1861765, oxBSeq_TMBD2-sc-1861766, oxBSeq_TMBD3-sc-1861767, oxBSeq_T_S_Exp10-sc-1861774, oxBSeq_T_S_Exp10-sc-1861775, oxBSeq_T_S_Exp11-sc-1861776, oxBSeq_T_S_Exp11-sc-1861777, oxBSeq_T_S_Exp16-sc-1861778, oxBSeq_T_S_Exp16-sc-1861779, pMEFAIDKO_BS-sc-2013-09-18T12:31:41Z-1692923, pMEFAIDKO_oxBS-sc-2013-09-18T12:31:54Z-1692925, pMEFWt_BS-sc-2013-09-18T12:31:34Z-1692922, pMEFWt_oxBS-sc-2013-09-18T12:31:48Z-1692924]

Track collection: Mouse methylome studies

+  All tracks in this collection (559)

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PMD       CpG methylation ▾       CpG reads ▾       AMR       HMR      
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experiment
ERX1246049 
ERX1246050 
ERX1246056 
ERX371615 
ERX371616 
ERX371617 
ERX371618 
ERX371619 
ERX371620 
ERX371621 
ERX371622 
ERX371623 
ERX371624 
ERX371625 
ERX371626 
ERX371627 
ERX371628 
ERX371629 
ERX371630 
ERX371631 
ERX371632 
ERX371633 
ERX371634 
ERX502124 
ERX502125 
ERX502126 
ERX502127 
ERX502128 
ERX502129 
ERX502130 
ERX502131 
ERX502132 
ERX502133 
ERX502134 
ERX502135 
ERX502136 
ERX502137 
ERX502138 
ERX502139 
ERX502140 
ERX502141 
ERX502142 
ERX502143 
ERX502144 
ERX502145 
ERX502146 
ERX502147 
ERX502151 
ERX502153 
ERX622633 
ERX622635 
ERX622636 
ERX622637 
ERX622638 
ERX625586 
ERX625587 
ERX625588 
ERX625589 
ERX625590 
ERX625591 
ERX634528 
ERX634529 
ERX634530 
ERX634531 
ERX634532 
ERX634533 
ERX634534 
ERX634535 
ERX634536 
ERX634537 
ERX634538 
ERX634539 
experiment
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 ERX1246049  HMR  2769STDY6182410-sc-2382182 / ERX1246049 (HMR)   Data format 
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 Configure 		 ERX1246049  CpG methylation  2769STDY6182410-sc-2382182 / ERX1246049 (CpG methylation)   Data format 
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 Configure 		 ERX1246050  CpG methylation  2769STDY6182411-sc-2382183 / ERX1246050 (CpG methylation)   Data format 
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 Configure 		 ERX1246056  CpG methylation  2769STDY6182411-sc-2382183 / ERX1246056 (CpG methylation)   Data format 
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 ERX371615  HMR  iPSC29_BS-sc-2013-09-18T12:30:24Z-1692910 / ERX371615 (HMR)   Data format 
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 Configure 		 ERX371615  CpG methylation  iPSC29_BS-sc-2013-09-18T12:30:24Z-1692910 / ERX371615 (CpG methylation)   Data format 
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 Configure 		 ERX371616  CpG methylation  iPSC28_BS-sc-2013-09-18T12:30:17Z-1692909 / ERX371616 (CpG methylation)   Data format 
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 ERX371617  HMR  iPSC27_BS-sc-2013-09-18T12:28:40Z-1692908 / ERX371617 (HMR)   Data format 
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 Configure 		 ERX371617  CpG methylation  iPSC27_BS-sc-2013-09-18T12:28:40Z-1692908 / ERX371617 (CpG methylation)   Data format 
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 ERX371618  HMR  iPSC29_oxBS-sc-2013-09-18T12:30:03Z-1692913 / ERX371618 (HMR)   Data format 
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 Configure 		 ERX371618  CpG methylation  iPSC29_oxBS-sc-2013-09-18T12:30:03Z-1692913 / ERX371618 (CpG methylation)   Data format 
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 Configure 		 ERX371619  CpG methylation  iPSC28_oxBS-sc-2013-09-18T12:29:53Z-1692912 / ERX371619 (CpG methylation)   Data format 
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 ERX371620  HMR  iPSC27_oxBS-sc-2013-09-18T12:29:46Z-1692911 / ERX371620 (HMR)   Data format 
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 Configure 		 ERX371620  CpG methylation  iPSC27_oxBS-sc-2013-09-18T12:29:46Z-1692911 / ERX371620 (CpG methylation)   Data format 
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 ERX371621  HMR  TMBD10_BS-sc-2013-09-18T12:28:21Z-1692906 / ERX371621 (HMR)   Data format 
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 Configure 		 ERX371621  CpG methylation  TMBD10_BS-sc-2013-09-18T12:28:21Z-1692906 / ERX371621 (CpG methylation)   Data format 
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 ERX371622  HMR  TMBD10_oxBS-sc-2013-09-18T12:28:31Z-1692907 / ERX371622 (HMR)   Data format 
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 Configure 		 ERX371622  CpG methylation  TMBD10_oxBS-sc-2013-09-18T12:28:31Z-1692907 / ERX371622 (CpG methylation)   Data format 
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 ERX371623  HMR  iPSC38_BS-sc-2013-09-18T12:31:20Z-1692917 / ERX371623 (HMR)   Data format 
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 Configure 		 ERX371623  CpG methylation  iPSC38_BS-sc-2013-09-18T12:31:20Z-1692917 / ERX371623 (CpG methylation)   Data format 
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 ERX371624  HMR  iPSC37_BS-sc-2013-09-18T12:31:14Z-1692916 / ERX371624 (HMR)   Data format 
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 Configure 		 ERX371624  CpG methylation  iPSC37_BS-sc-2013-09-18T12:31:14Z-1692916 / ERX371624 (CpG methylation)   Data format 
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 ERX371625  HMR  iPSC20_BS-sc-2013-09-18T12:31:06Z-1692915 / ERX371625 (HMR)   Data format 
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 Configure 		 ERX371625  CpG methylation  iPSC20_BS-sc-2013-09-18T12:31:06Z-1692915 / ERX371625 (CpG methylation)   Data format 
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 ERX371626  HMR  iPSC19_BS-sc-2013-09-18T12:30:10Z-1692914 / ERX371626 (HMR)   Data format 
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 Configure 		 ERX371626  CpG methylation  iPSC19_BS-sc-2013-09-18T12:30:10Z-1692914 / ERX371626 (CpG methylation)   Data format 
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 ERX371627  HMR  iPSC38_oxBS-sc-2013-09-18T12:30:43Z-1692921 / ERX371627 (HMR)   Data format 
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 Configure 		 ERX371627  CpG methylation  iPSC38_oxBS-sc-2013-09-18T12:30:43Z-1692921 / ERX371627 (CpG methylation)   Data format 
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 ERX371628  HMR  iPSC37_oxBS-sc-2013-09-18T12:30:37Z-1692920 / ERX371628 (HMR)   Data format 
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 Configure 		 ERX371628  CpG methylation  iPSC37_oxBS-sc-2013-09-18T12:30:37Z-1692920 / ERX371628 (CpG methylation)   Data format 
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 ERX371629  HMR  iPSC20_oxBS-sc-2013-09-18T12:30:31Z-1692919 / ERX371629 (HMR)   Data format 
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 Configure 		 ERX371629  CpG methylation  iPSC20_oxBS-sc-2013-09-18T12:30:31Z-1692919 / ERX371629 (CpG methylation)   Data format 
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 ERX371630  HMR  iPSC19_oxBS-sc-2013-09-18T12:31:26Z-1692918 / ERX371630 (HMR)   Data format 
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 Configure 		 ERX371630  CpG methylation  iPSC19_oxBS-sc-2013-09-18T12:31:26Z-1692918 / ERX371630 (CpG methylation)   Data format 
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 ERX371631  HMR  pMEFWt_BS-sc-2013-09-18T12:31:34Z-1692922 / ERX371631 (HMR)   Data format 
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 Configure 		 ERX371631  CpG methylation  pMEFWt_BS-sc-2013-09-18T12:31:34Z-1692922 / ERX371631 (CpG methylation)   Data format 
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 ERX371632  HMR  pMEFAIDKO_BS-sc-2013-09-18T12:31:41Z-1692923 / ERX371632 (HMR)   Data format 
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 Configure 		 ERX371632  CpG methylation  pMEFAIDKO_BS-sc-2013-09-18T12:31:41Z-1692923 / ERX371632 (CpG methylation)   Data format 
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 ERX371633  HMR  pMEFWt_oxBS-sc-2013-09-18T12:31:48Z-1692924 / ERX371633 (HMR)   Data format 
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 Configure 		 ERX371633  CpG methylation  pMEFWt_oxBS-sc-2013-09-18T12:31:48Z-1692924 / ERX371633 (CpG methylation)   Data format 
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 ERX371634  HMR  pMEFAIDKO_oxBS-sc-2013-09-18T12:31:54Z-1692925 / ERX371634 (HMR)   Data format 
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 Configure 		 ERX371634  CpG methylation  pMEFAIDKO_oxBS-sc-2013-09-18T12:31:54Z-1692925 / ERX371634 (CpG methylation)   Data format 
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 ERX502124  HMR  BSeq_MEF1-sc-1861756 / ERX502124 (HMR)   Data format 
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 Configure 		 ERX502124  CpG methylation  BSeq_MEF1-sc-1861756 / ERX502124 (CpG methylation)   Data format 
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 ERX502125  HMR  BSeq_MEF2-sc-1861757 / ERX502125 (HMR)   Data format 
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 Configure 		 ERX502125  CpG methylation  BSeq_MEF2-sc-1861757 / ERX502125 (CpG methylation)   Data format 
hide
 ERX502126  HMR  BSeq_MEF3-sc-1861758 / ERX502126 (HMR)   Data format 
hide
 Configure 		 ERX502126  CpG methylation  BSeq_MEF3-sc-1861758 / ERX502126 (CpG methylation)   Data format 
hide
 ERX502127  HMR  BSeq_TMBD1-sc-1861759 / ERX502127 (HMR)   Data format 
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 Configure 		 ERX502127  CpG methylation  BSeq_TMBD1-sc-1861759 / ERX502127 (CpG methylation)   Data format 
hide
 ERX502128  HMR  BSeq_TMBD2-sc-1861760 / ERX502128 (HMR)   Data format 
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 Configure 		 ERX502128  CpG methylation  BSeq_TMBD2-sc-1861760 / ERX502128 (CpG methylation)   Data format 
hide
 ERX502129  HMR  BSeq_TMBD3-sc-1861761 / ERX502129 (HMR)   Data format 
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 Configure 		 ERX502129  CpG methylation  BSeq_TMBD3-sc-1861761 / ERX502129 (CpG methylation)   Data format 
hide
 ERX502130  HMR  oxBSeq_MEF1-sc-1861762 / ERX502130 (HMR)   Data format 
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 Configure 		 ERX502130  CpG methylation  oxBSeq_MEF1-sc-1861762 / ERX502130 (CpG methylation)   Data format 
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 ERX502131  HMR  oxBSeq_MEF2-sc-1861763 / ERX502131 (HMR)   Data format 
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 Configure 		 ERX502131  CpG methylation  oxBSeq_MEF2-sc-1861763 / ERX502131 (CpG methylation)   Data format 
hide
 ERX502132  HMR  oxBSeq_MEF3-sc-1861764 / ERX502132 (HMR)   Data format 
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 Configure 		 ERX502132  CpG methylation  oxBSeq_MEF3-sc-1861764 / ERX502132 (CpG methylation)   Data format 
hide
 ERX502133  HMR  oxBSeq_TMBD1-sc-1861765 / ERX502133 (HMR)   Data format 
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 Configure 		 ERX502133  CpG methylation  oxBSeq_TMBD1-sc-1861765 / ERX502133 (CpG methylation)   Data format 
hide
 ERX502134  HMR  oxBSeq_TMBD2-sc-1861766 / ERX502134 (HMR)   Data format 
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 Configure 		 ERX502134  CpG methylation  oxBSeq_TMBD2-sc-1861766 / ERX502134 (CpG methylation)   Data format 
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 ERX502135  HMR  oxBSeq_TMBD3-sc-1861767 / ERX502135 (HMR)   Data format 
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 Configure 		 ERX502135  CpG methylation  oxBSeq_TMBD3-sc-1861767 / ERX502135 (CpG methylation)   Data format 
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 Configure 		 ERX502136  CpG methylation  BSeq_T_S_Exp10-sc-1861768 / ERX502136 (CpG methylation)   Data format 
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 Configure 		 ERX502137  CpG methylation  BSeq_T_S_Exp11-sc-1861770 / ERX502137 (CpG methylation)   Data format 
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 Configure 		 ERX502138  CpG methylation  BSeq_T_S_Exp16-sc-1861772 / ERX502138 (CpG methylation)   Data format 
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 Configure 		 ERX502139  CpG methylation  BSeq_T_S_Exp10-sc-1861769 / ERX502139 (CpG methylation)   Data format 
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 Configure 		 ERX502140  CpG methylation  BSeq_T_S_Exp11-sc-1861771 / ERX502140 (CpG methylation)   Data format 
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 Configure 		 ERX502141  CpG methylation  BSeq_T_S_Exp16-sc-1861773 / ERX502141 (CpG methylation)   Data format 
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 Configure 		 ERX502142  CpG methylation  oxBSeq_T_S_Exp10-sc-1861774 / ERX502142 (CpG methylation)   Data format 
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 Configure 		 ERX502143  CpG methylation  oxBSeq_T_S_Exp11-sc-1861776 / ERX502143 (CpG methylation)   Data format 
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 Configure 		 ERX502144  CpG methylation  oxBSeq_T_S_Exp16-sc-1861778 / ERX502144 (CpG methylation)   Data format 
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 Configure 		 ERX502145  CpG methylation  oxBSeq_T_S_Exp10-sc-1861775 / ERX502145 (CpG methylation)   Data format 
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 Configure 		 ERX502146  CpG methylation  oxBSeq_T_S_Exp11-sc-1861777 / ERX502146 (CpG methylation)   Data format 
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 Configure 		 ERX502147  CpG methylation  oxBSeq_T_S_Exp16-sc-1861779 / ERX502147 (CpG methylation)   Data format 
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 Configure 		 ERX502151  CpG methylation  BSeq_P8_iPSC67-sc-1861783 / ERX502151 (CpG methylation)   Data format 
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 Configure 		 ERX502153  CpG methylation  BSeq_P8_iPSC73-sc-1861785 / ERX502153 (CpG methylation)   Data format 
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 Configure 		 ERX622633  CpG methylation  BSeq_P29_iPSC44-sc-2014730 / ERX622633 (CpG methylation)   Data format 
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 ERX622635  HMR  BSeq_P29_iPSC66-sc-2014732 / ERX622635 (HMR)   Data format 
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 Configure 		 ERX622635  CpG methylation  BSeq_P29_iPSC66-sc-2014732 / ERX622635 (CpG methylation)   Data format 
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 Configure 		 ERX622636  CpG methylation  BSeq_P29_iPSC67-sc-2014733 / ERX622636 (CpG methylation)   Data format 
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 ERX622637  HMR  BSeq_P29_iPSC72-sc-2014734 / ERX622637 (HMR)   Data format 
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 Configure 		 ERX622637  CpG methylation  BSeq_P29_iPSC72-sc-2014734 / ERX622637 (CpG methylation)   Data format 
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 Configure 		 ERX622638  CpG methylation  BSeq_P29_iPSC73-sc-2014735 / ERX622638 (CpG methylation)   Data format 
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 Configure 		 ERX625586  CpG methylation  oxBSeq_P29_iPSC44-sc-2014736 / ERX625586 (CpG methylation)   Data format 
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 Configure 		 ERX625587  CpG methylation  oxBSeq_P29_iPSC45-sc-2014737 / ERX625587 (CpG methylation)   Data format 
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 Configure 		 ERX625588  CpG methylation  oxBSeq_P29_iPSC66-sc-2014738 / ERX625588 (CpG methylation)   Data format 
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 Configure 		 ERX625589  CpG methylation  oxBSeq_P29_iPSC67-sc-2014739 / ERX625589 (CpG methylation)   Data format 
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 ERX625590  HMR  oxBSeq_P29_iPSC72-sc-2014740 / ERX625590 (HMR)   Data format 
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 Configure 		 ERX625590  CpG methylation  oxBSeq_P29_iPSC72-sc-2014740 / ERX625590 (CpG methylation)   Data format 
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 Configure 		 ERX625591  CpG methylation  oxBSeq_P29_iPSC73-sc-2014741 / ERX625591 (CpG methylation)   Data format 
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 Configure 		 ERX634528  CpG methylation  BSeq_P29_iPSC44-sc-2014730 / ERX634528 (CpG methylation)   Data format 
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 Configure 		 ERX634529  CpG methylation  BSeq_P29_iPSC45-sc-2014731 / ERX634529 (CpG methylation)   Data format 
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 Configure 		 ERX634530  CpG methylation  BSeq_P29_iPSC66-sc-2014732 / ERX634530 (CpG methylation)   Data format 
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 Configure 		 ERX634531  CpG methylation  BSeq_P29_iPSC67-sc-2014733 / ERX634531 (CpG methylation)   Data format 
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 ERX634532  HMR  BSeq_P29_iPSC72-sc-2014734 / ERX634532 (HMR)   Data format 
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 Configure 		 ERX634532  CpG methylation  BSeq_P29_iPSC72-sc-2014734 / ERX634532 (CpG methylation)   Data format 
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 Configure 		 ERX634533  CpG methylation  BSeq_P29_iPSC73-sc-2014735 / ERX634533 (CpG methylation)   Data format 
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 Configure 		 ERX634534  CpG methylation  oxBSeq_P29_iPSC44-sc-2014736 / ERX634534 (CpG methylation)   Data format 
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 Configure 		 ERX634535  CpG methylation  oxBSeq_P29_iPSC45-sc-2014737 / ERX634535 (CpG methylation)   Data format 
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 Configure 		 ERX634536  CpG methylation  oxBSeq_P29_iPSC66-sc-2014738 / ERX634536 (CpG methylation)   Data format 
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 Configure 		 ERX634537  CpG methylation  oxBSeq_P29_iPSC67-sc-2014739 / ERX634537 (CpG methylation)   Data format 
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 ERX634538  HMR  oxBSeq_P29_iPSC72-sc-2014740 / ERX634538 (HMR)   Data format 
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 Configure 		 ERX634538  CpG methylation  oxBSeq_P29_iPSC72-sc-2014740 / ERX634538 (CpG methylation)   Data format 
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 Configure 		 ERX634539  CpG methylation  oxBSeq_P29_iPSC73-sc-2014741 / ERX634539 (CpG methylation)   Data format 
    
Assembly: Mouse Jun. 2020 (GRCm39/mm39)

Study title: Methylome_and_Hydroxymethylome_of_iPSC
SRA: ERP003907
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Title
ERX1246049 2769STDY6182410-sc-2382182 0.692 1.8 21671 2030.2 0 0.0 283 56651.9 0.992 Illumina HiSeq 2500 paired end sequencing
ERX1246050 2769STDY6182411-sc-2382183 0.381 1.8 0 0.0 0 0.0 1 41725280.0 0.993 Illumina HiSeq 2500 paired end sequencing
ERX1246056 2769STDY6182411-sc-2382183 0.382 1.7 3 613500.3 0 0.0 0 0.0 0.993 Illumina HiSeq 2500 paired end sequencing
ERX371615 iPSC29_BS-sc-2013-09-18T12:30:24Z-1692910 0.608 2.7 25162 2075.2 0 0.0 532 42484.6 0.996 Illumina HiSeq 2000 paired end sequencing
ERX371616 iPSC28_BS-sc-2013-09-18T12:30:17Z-1692909 0.277 2.7 2 850454.5 0 0.0 0 0.0 0.997 Illumina HiSeq 2000 paired end sequencing
ERX371617 iPSC27_BS-sc-2013-09-18T12:28:40Z-1692908 0.637 2.6 23770 1709.5 0 0.0 538 34189.3 0.995 Illumina HiSeq 2000 paired end sequencing
ERX371618 iPSC29_oxBS-sc-2013-09-18T12:30:03Z-1692913 0.593 2.1 23029 2781.0 0 0.0 571 61797.4 0.996 Illumina HiSeq 2000 paired end sequencing
ERX371619 iPSC28_oxBS-sc-2013-09-18T12:29:53Z-1692912 0.262 2.1 1 730206.0 0 0.0 1 33790000.0 0.997 Illumina HiSeq 2000 paired end sequencing
ERX371620 iPSC27_oxBS-sc-2013-09-18T12:29:46Z-1692911 0.625 2.1 22200 2141.5 0 0.0 367 51320.3 0.995 Illumina HiSeq 2000 paired end sequencing
ERX371621 TMBD10_BS-sc-2013-09-18T12:28:21Z-1692906 0.730 5.5 31315 1268.5 25 991.0 1806 14986.4 0.994 Illumina HiSeq 2000 paired end sequencing
ERX371622 TMBD10_oxBS-sc-2013-09-18T12:28:31Z-1692907 0.716 4.3 31698 1340.0 28 1129.8 1263 23330.6 0.994 Illumina HiSeq 2000 paired end sequencing
ERX371623 iPSC38_BS-sc-2013-09-18T12:31:20Z-1692917 0.625 2.1 21129 2178.0 0 0.0 401 45059.4 0.996 Illumina HiSeq 2000 paired end sequencing
ERX371624 iPSC37_BS-sc-2013-09-18T12:31:14Z-1692916 0.647 2.1 22522 1923.6 0 0.0 239 50856.8 0.995 Illumina HiSeq 2000 paired end sequencing
ERX371625 iPSC20_BS-sc-2013-09-18T12:31:06Z-1692915 0.560 1.8 20203 2083.3 1 568.0 0 0.0 0.996 Illumina HiSeq 2000 paired end sequencing
ERX371626 iPSC19_BS-sc-2013-09-18T12:30:10Z-1692914 0.640 1.9 22521 2165.8 0 0.0 353 63057.1 0.994 Illumina HiSeq 2000 paired end sequencing
ERX371627 iPSC38_oxBS-sc-2013-09-18T12:30:43Z-1692921 0.616 1.9 20843 2416.8 0 0.0 312 62697.8 0.996 Illumina HiSeq 2000 paired end sequencing
ERX371628 iPSC37_oxBS-sc-2013-09-18T12:30:37Z-1692920 0.637 1.9 21910 2165.8 0 0.0 350 55387.9 0.995 Illumina HiSeq 2000 paired end sequencing
ERX371629 iPSC20_oxBS-sc-2013-09-18T12:30:31Z-1692919 0.552 1.7 20047 2096.0 1 674.0 0 0.0 0.997 Illumina HiSeq 2000 paired end sequencing
ERX371630 iPSC19_oxBS-sc-2013-09-18T12:31:26Z-1692918 0.626 1.8 21635 2473.1 0 0.0 497 70369.2 0.994 Illumina HiSeq 2000 paired end sequencing
ERX371631 pMEFWt_BS-sc-2013-09-18T12:31:34Z-1692922 0.620 3.5 26928 1582.9 0 0.0 330 23373.7 0.999 Illumina HiSeq 2000 paired end sequencing
ERX371632 pMEFAIDKO_BS-sc-2013-09-18T12:31:41Z-1692923 0.641 4.1 27428 1437.0 2 907.5 398 23093.3 0.999 Illumina HiSeq 2000 paired end sequencing
ERX371633 pMEFWt_oxBS-sc-2013-09-18T12:31:48Z-1692924 0.614 3.1 24653 1794.6 0 0.0 286 26848.5 0.999 Illumina HiSeq 2000 paired end sequencing
ERX371634 pMEFAIDKO_oxBS-sc-2013-09-18T12:31:54Z-1692925 0.639 3.6 27083 1495.1 4 973.8 407 21962.9 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502124 BSeq_MEF1-sc-1861756 0.615 2.5 21569 2094.5 0 0.0 320 31663.7 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502125 BSeq_MEF2-sc-1861757 0.633 2.4 25943 1853.7 0 0.0 398 31181.0 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502126 BSeq_MEF3-sc-1861758 0.619 2.5 24259 1918.7 0 0.0 288 31985.3 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502127 BSeq_TMBD1-sc-1861759 0.635 2.5 25540 1721.2 0 0.0 331 42929.1 0.994 Illumina HiSeq 2000 paired end sequencing
ERX502128 BSeq_TMBD2-sc-1861760 0.665 2.2 23430 1646.6 0 0.0 410 39782.9 0.995 Illumina HiSeq 2000 paired end sequencing
ERX502129 BSeq_TMBD3-sc-1861761 0.661 2.5 24822 1547.8 1 1733.0 312 38651.4 0.995 Illumina HiSeq 2000 paired end sequencing
ERX502130 oxBSeq_MEF1-sc-1861762 0.609 2.3 20908 2289.3 0 0.0 198 43181.9 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502131 oxBSeq_MEF2-sc-1861763 0.628 2.3 23705 1993.3 0 0.0 344 36251.8 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502132 oxBSeq_MEF3-sc-1861764 0.617 2.4 22875 2032.8 0 0.0 318 30661.2 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502133 oxBSeq_TMBD1-sc-1861765 0.627 2.1 23572 2031.1 0 0.0 366 56212.7 0.994 Illumina HiSeq 2000 paired end sequencing
ERX502134 oxBSeq_TMBD2-sc-1861766 0.653 2.2 24508 1662.7 1 1097.0 448 39933.2 0.995 Illumina HiSeq 2000 paired end sequencing
ERX502135 oxBSeq_TMBD3-sc-1861767 0.648 2.3 24402 1691.6 2 968.5 457 41356.1 0.995 Illumina HiSeq 2000 paired end sequencing
ERX502136 BSeq_T_S_Exp10-sc-1861768 0.596 2.2 19882 3084.5 0 0.0 424 1773914.8 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502137 BSeq_T_S_Exp11-sc-1861770 0.600 2.3 19764 2637.5 0 0.0 160 57899.2 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502138 BSeq_T_S_Exp16-sc-1861772 0.591 2.3 19440 3172.1 0 0.0 513 1489791.6 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502139 BSeq_T_S_Exp10-sc-1861769 0.565 2.2 18683 3640.9 1 928.0 533 1313128.5 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502140 BSeq_T_S_Exp11-sc-1861771 0.578 2.2 18639 3127.8 0 0.0 745 445530.1 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502141 BSeq_T_S_Exp16-sc-1861773 0.569 2.1 18291 3635.4 0 0.0 521 1354801.7 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502142 oxBSeq_T_S_Exp10-sc-1861774 0.591 2.1 19180 3127.5 0 0.0 373 1875856.4 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502143 oxBSeq_T_S_Exp11-sc-1861776 0.597 2.1 19163 2779.1 0 0.0 108 82896.6 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502144 oxBSeq_T_S_Exp16-sc-1861778 0.588 2.3 19200 3203.0 0 0.0 489 1531601.1 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502145 oxBSeq_T_S_Exp10-sc-1861775 0.555 2.2 18193 3623.3 1 901.0 560 1205334.1 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502146 oxBSeq_T_S_Exp11-sc-1861777 0.566 2.2 18298 3229.7 1 584.0 383 165477.1 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502147 oxBSeq_T_S_Exp16-sc-1861779 0.557 2.2 18464 3713.7 0 0.0 562 1208502.1 0.999 Illumina HiSeq 2000 paired end sequencing
ERX502151 BSeq_P8_iPSC67-sc-1861783 0.393 1.5 1 655133.0 0 0.0 21 9304185.1 0.996 Illumina HiSeq 2000 paired end sequencing
ERX502153 BSeq_P8_iPSC73-sc-1861785 0.431 1.5 1 672916.0 0 0.0 96 213249.2 0.996 Illumina HiSeq 2000 paired end sequencing
ERX622633 BSeq_P29_iPSC44-sc-2014730 0.195 1.5 1 631824.0 0 0.0 1 109669217.0 0.998 Illumina HiSeq 2000 paired end sequencing
ERX622635 BSeq_P29_iPSC66-sc-2014732 0.554 1.6 22734 2953.7 0 0.0 441 102173.3 0.997 Illumina HiSeq 2000 paired end sequencing
ERX622636 BSeq_P29_iPSC67-sc-2014733 0.443 1.4 0 0.0 0 0.0 241 198054.5 0.998 Illumina HiSeq 2000 paired end sequencing
ERX622637 BSeq_P29_iPSC72-sc-2014734 0.562 1.5 23406 2275.7 0 0.0 200 110536.4 0.996 Illumina HiSeq 2000 paired end sequencing
ERX622638 BSeq_P29_iPSC73-sc-2014735 0.277 1.5 0 0.0 0 0.0 745 1648693.8 1.000 Illumina HiSeq 2000 paired end sequencing
ERX625586 oxBSeq_P29_iPSC44-sc-2014736 0.188 1.5 1 714527.0 0 0.0 0 0.0 0.998 Illumina HiSeq 2000 paired end sequencing
ERX625587 oxBSeq_P29_iPSC45-sc-2014737 0.267 1.6 1 838820.0 0 0.0 5 18725852.8 0.998 Illumina HiSeq 2000 paired end sequencing
ERX625588 oxBSeq_P29_iPSC66-sc-2014738 0.540 1.5 23884 3127.2 1 564.0 475 118367.9 0.997 Illumina HiSeq 2000 paired end sequencing
ERX625589 oxBSeq_P29_iPSC67-sc-2014739 0.424 1.5 2 642479.5 0 0.0 467 190628.7 0.998 Illumina HiSeq 2000 paired end sequencing
ERX625590 oxBSeq_P29_iPSC72-sc-2014740 0.552 1.5 23915 2398.2 0 0.0 299 111413.6 0.996 Illumina HiSeq 2000 paired end sequencing
ERX625591 oxBSeq_P29_iPSC73-sc-2014741 0.276 1.6 0 0.0 0 0.0 803 1550549.9 1.000 Illumina HiSeq 2000 paired end sequencing
ERX634528 BSeq_P29_iPSC44-sc-2014730 0.190 2.4 2 877087.0 0 0.0 0 0.0 0.998 Illumina HiSeq 2000 paired end sequencing
ERX634529 BSeq_P29_iPSC45-sc-2014731 0.274 2.2 2 857164.5 0 0.0 6 12285332.5 0.998 Illumina HiSeq 2000 paired end sequencing
ERX634530 BSeq_P29_iPSC66-sc-2014732 0.547 2.5 22331 3147.0 0 0.0 494 53685.6 0.997 Illumina HiSeq 2000 paired end sequencing
ERX634531 BSeq_P29_iPSC67-sc-2014733 0.436 2.3 1671 16184.4 1 670.0 576 74617.0 0.998 Illumina HiSeq 2000 paired end sequencing
ERX634532 BSeq_P29_iPSC72-sc-2014734 0.554 2.3 21739 2775.3 0 0.0 450 41219.6 0.996 Illumina HiSeq 2000 paired end sequencing
ERX634533 BSeq_P29_iPSC73-sc-2014735 0.266 2.4 0 0.0 0 0.0 977 1321603.5 0.999 Illumina HiSeq 2000 paired end sequencing
ERX634534 oxBSeq_P29_iPSC44-sc-2014736 0.183 2.1 1 915240.0 0 0.0 0 0.0 0.998 Illumina HiSeq 2000 paired end sequencing
ERX634535 oxBSeq_P29_iPSC45-sc-2014737 0.261 2.3 2 965308.5 0 0.0 12 7710416.1 0.998 Illumina HiSeq 2000 paired end sequencing
ERX634536 oxBSeq_P29_iPSC66-sc-2014738 0.531 2.2 22657 3544.2 0 0.0 388 81681.9 0.997 Illumina HiSeq 2000 paired end sequencing
ERX634537 oxBSeq_P29_iPSC67-sc-2014739 0.416 2.1 0 0.0 2 716.5 442 115631.1 0.998 Illumina HiSeq 2000 paired end sequencing
ERX634538 oxBSeq_P29_iPSC72-sc-2014740 0.543 2.1 22294 2927.2 1 502.0 464 54450.5 0.996 Illumina HiSeq 2000 paired end sequencing
ERX634539 oxBSeq_P29_iPSC73-sc-2014741 0.267 2.4 0 0.0 0 0.0 978 1313523.4 0.999 Illumina HiSeq 2000 paired end sequencing

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.