Human methylome studies SRP217135 Track Settings
 
Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [WGBS] [CD4, Neutrophils, Whole Blood]

Track collection: Human methylome studies

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 SRX6640718  HMR  Whole Blood / SRX6640718 (HMR)   Data format 
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 SRX6640718  CpG methylation  Whole Blood / SRX6640718 (CpG methylation)   Data format 
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 SRX6640719  CpG methylation  Whole Blood / SRX6640719 (CpG methylation)   Data format 
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 SRX6640720  HMR  Whole Blood / SRX6640720 (HMR)   Data format 
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 SRX6640720  CpG methylation  Whole Blood / SRX6640720 (CpG methylation)   Data format 
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 SRX6640721  HMR  Whole Blood / SRX6640721 (HMR)   Data format 
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 SRX6640721  CpG methylation  Whole Blood / SRX6640721 (CpG methylation)   Data format 
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 SRX6640722  HMR  Whole Blood / SRX6640722 (HMR)   Data format 
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 SRX6640722  CpG methylation  Whole Blood / SRX6640722 (CpG methylation)   Data format 
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 SRX6640723  HMR  Whole Blood / SRX6640723 (HMR)   Data format 
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 SRX6640723  CpG methylation  Whole Blood / SRX6640723 (CpG methylation)   Data format 
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 SRX6640724  HMR  Whole Blood / SRX6640724 (HMR)   Data format 
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 SRX6640724  CpG methylation  Whole Blood / SRX6640724 (CpG methylation)   Data format 
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 SRX6640725  HMR  Whole Blood / SRX6640725 (HMR)   Data format 
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 SRX6640725  CpG methylation  Whole Blood / SRX6640725 (CpG methylation)   Data format 
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 SRX6640726  HMR  Whole Blood / SRX6640726 (HMR)   Data format 
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 SRX6640726  CpG methylation  Whole Blood / SRX6640726 (CpG methylation)   Data format 
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 SRX6640727  HMR  Whole Blood / SRX6640727 (HMR)   Data format 
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 SRX6640727  CpG methylation  Whole Blood / SRX6640727 (CpG methylation)   Data format 
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 SRX6640728  HMR  Whole Blood / SRX6640728 (HMR)   Data format 
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 SRX6640728  CpG methylation  Whole Blood / SRX6640728 (CpG methylation)   Data format 
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 SRX6640729  HMR  Whole Blood / SRX6640729 (HMR)   Data format 
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 SRX6640729  CpG methylation  Whole Blood / SRX6640729 (CpG methylation)   Data format 
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 SRX6640730  HMR  Whole Blood / SRX6640730 (HMR)   Data format 
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 SRX6640730  CpG methylation  Whole Blood / SRX6640730 (CpG methylation)   Data format 
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 SRX6640731  HMR  Whole Blood / SRX6640731 (HMR)   Data format 
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 SRX6640731  CpG methylation  Whole Blood / SRX6640731 (CpG methylation)   Data format 
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 SRX6640732  HMR  Whole Blood / SRX6640732 (HMR)   Data format 
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 SRX6640732  CpG methylation  Whole Blood / SRX6640732 (CpG methylation)   Data format 
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 SRX6640733  HMR  Whole Blood / SRX6640733 (HMR)   Data format 
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 SRX6640733  CpG methylation  Whole Blood / SRX6640733 (CpG methylation)   Data format 
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 SRX6640734  HMR  Whole Blood / SRX6640734 (HMR)   Data format 
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 SRX6640734  CpG methylation  Whole Blood / SRX6640734 (CpG methylation)   Data format 
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 SRX6640735  HMR  Whole Blood / SRX6640735 (HMR)   Data format 
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 SRX6640735  CpG methylation  Whole Blood / SRX6640735 (CpG methylation)   Data format 
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 SRX6640736  HMR  Whole Blood / SRX6640736 (HMR)   Data format 
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 SRX6640736  CpG methylation  Whole Blood / SRX6640736 (CpG methylation)   Data format 
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 SRX6640737  HMR  Whole Blood / SRX6640737 (HMR)   Data format 
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 SRX6640737  CpG methylation  Whole Blood / SRX6640737 (CpG methylation)   Data format 
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 SRX6640738  HMR  Whole Blood / SRX6640738 (HMR)   Data format 
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 SRX6640738  CpG methylation  Whole Blood / SRX6640738 (CpG methylation)   Data format 
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 SRX6640739  HMR  Whole Blood / SRX6640739 (HMR)   Data format 
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 SRX6640739  CpG methylation  Whole Blood / SRX6640739 (CpG methylation)   Data format 
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 SRX6640740  HMR  Whole Blood / SRX6640740 (HMR)   Data format 
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 SRX6640740  CpG methylation  Whole Blood / SRX6640740 (CpG methylation)   Data format 
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 SRX6640741  HMR  Whole Blood / SRX6640741 (HMR)   Data format 
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 SRX6640741  CpG methylation  Whole Blood / SRX6640741 (CpG methylation)   Data format 
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 SRX6640742  HMR  Whole Blood / SRX6640742 (HMR)   Data format 
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 SRX6640742  CpG methylation  Whole Blood / SRX6640742 (CpG methylation)   Data format 
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 SRX6640743  HMR  CD4 / SRX6640743 (HMR)   Data format 
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 SRX6640743  CpG methylation  CD4 / SRX6640743 (CpG methylation)   Data format 
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 SRX6640744  HMR  CD4 / SRX6640744 (HMR)   Data format 
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 SRX6640744  CpG methylation  CD4 / SRX6640744 (CpG methylation)   Data format 
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 SRX6640745  HMR  CD4 / SRX6640745 (HMR)   Data format 
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 SRX6640745  CpG methylation  CD4 / SRX6640745 (CpG methylation)   Data format 
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 SRX6640746  HMR  CD4 / SRX6640746 (HMR)   Data format 
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 SRX6640746  CpG methylation  CD4 / SRX6640746 (CpG methylation)   Data format 
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 SRX6640747  HMR  Neutrophils / SRX6640747 (HMR)   Data format 
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 SRX6640747  CpG methylation  Neutrophils / SRX6640747 (CpG methylation)   Data format 
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 SRX6640748  HMR  Neutrophils / SRX6640748 (HMR)   Data format 
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 SRX6640748  CpG methylation  Neutrophils / SRX6640748 (CpG methylation)   Data format 
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 SRX6640749  HMR  Neutrophils / SRX6640749 (HMR)   Data format 
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 SRX6640749  CpG methylation  Neutrophils / SRX6640749 (CpG methylation)   Data format 
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 SRX6640750  HMR  Neutrophils / SRX6640750 (HMR)   Data format 
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 SRX6640750  CpG methylation  Neutrophils / SRX6640750 (CpG methylation)   Data format 
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 SRX6640751  HMR  Neutrophils / SRX6640751 (HMR)   Data format 
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 SRX6640751  CpG methylation  Neutrophils / SRX6640751 (CpG methylation)   Data format 
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 SRX6640752  HMR  Neutrophils / SRX6640752 (HMR)   Data format 
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 SRX6640752  CpG methylation  Neutrophils / SRX6640752 (CpG methylation)   Data format 
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 SRX6640753  HMR  Neutrophils / SRX6640753 (HMR)   Data format 
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 SRX6640753  CpG methylation  Neutrophils / SRX6640753 (CpG methylation)   Data format 
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 SRX6640754  HMR  Neutrophils / SRX6640754 (HMR)   Data format 
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 SRX6640754  CpG methylation  Neutrophils / SRX6640754 (CpG methylation)   Data format 
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 SRX6640755  HMR  CD4 / SRX6640755 (HMR)   Data format 
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 SRX6640755  CpG methylation  CD4 / SRX6640755 (CpG methylation)   Data format 
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 SRX6640756  HMR  CD4 / SRX6640756 (HMR)   Data format 
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 SRX6640756  CpG methylation  CD4 / SRX6640756 (CpG methylation)   Data format 
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 SRX6640757  HMR  CD4 / SRX6640757 (HMR)   Data format 
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 SRX6640757  CpG methylation  CD4 / SRX6640757 (CpG methylation)   Data format 
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 SRX6640758  HMR  CD4 / SRX6640758 (HMR)   Data format 
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 SRX6640758  CpG methylation  CD4 / SRX6640758 (CpG methylation)   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

Study title: Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [WGBS]
SRA: SRP217135
GEO: GSE128731
Pubmed: 31316107

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Title
SRX6640718 Whole Blood 0.782 39.6 66059 1009.0 3420 976.8 3640 10297.6 0.986 GSM3683951: Sample1_Swift_NovaSeq; Homo sapiens; Bisulfite-Seq
SRX6640719 Whole Blood 0.662 31.4 62253 897.3 2332 984.0 3270 8713.4 0.994 GSM3683952: Sample1_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640720 Whole Blood 0.786 28.7 62699 1018.6 3035 983.3 3303 10292.8 0.986 GSM3683953: Sample1_Swift_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640721 Whole Blood 0.757 23.2 48465 1028.4 2669 1006.1 1208 14405.7 0.985 GSM3683954: Sample1_TruSeq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640722 Whole Blood 0.795 39.0 71288 953.3 1575 836.1 4402 10483.7 0.986 GSM3683955: Sample2_Swift_NovaSeq_rep1; Homo sapiens; Bisulfite-Seq
SRX6640723 Whole Blood 0.807 45.7 71270 998.4 1658 841.9 3541 12202.2 0.987 GSM3683956: Sample2_Swift_NovaSeq_rep2; Homo sapiens; Bisulfite-Seq
SRX6640724 Whole Blood 0.651 27.2 63654 854.6 1094 893.7 3312 8465.5 0.993 GSM3683957: Sample2_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640725 Whole Blood 0.799 28.0 68992 954.5 1396 838.6 3565 11166.7 0.986 GSM3683958: Sample2_Swift_HiSeqX_rep1; Homo sapiens; Bisulfite-Seq
SRX6640726 Whole Blood 0.810 28.2 67655 996.4 1315 840.0 3666 11351.5 0.987 GSM3683959: Sample2_Swift_HiSeqX_rep2; Homo sapiens; Bisulfite-Seq
SRX6640727 Whole Blood 0.767 24.7 56801 958.6 1585 890.0 1517 13850.3 0.979 GSM3683960: Sample2_TruSeq_HiSeqX_rep1; Homo sapiens; Bisulfite-Seq
SRX6640728 Whole Blood 0.777 17.6 55402 1004.0 1139 898.0 1807 14558.6 0.974 GSM3683961: Sample2_TruSeq_HiSeqX_rep2; Homo sapiens; Bisulfite-Seq
SRX6640729 Whole Blood 0.797 37.8 70831 996.8 2248 992.8 3782 12953.5 0.985 GSM3683962: Sample3_Swift_NovaSeq_rep1; Homo sapiens; Bisulfite-Seq
SRX6640730 Whole Blood 0.809 41.9 69363 1043.1 2464 980.6 4071 12664.2 0.987 GSM3683963: Sample3_Swift_NovaSeq_rep2; Homo sapiens; Bisulfite-Seq
SRX6640731 Whole Blood 0.674 24.6 64839 863.4 1515 1021.9 3095 9831.1 0.989 GSM3683964: Sample3_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640732 Whole Blood 0.802 27.6 69065 986.2 2030 996.1 3857 12212.9 0.985 GSM3683965: Sample3_Swift_HiSeqX_rep1; Homo sapiens; Bisulfite-Seq
SRX6640733 Whole Blood 0.811 23.6 65861 1015.8 1842 978.0 3579 12487.1 0.987 GSM3683966: Sample3_Swift_HiSeqX_rep2; Homo sapiens; Bisulfite-Seq
SRX6640734 Whole Blood 0.771 24.3 59180 925.1 2239 1002.7 1622 15234.6 0.984 GSM3683967: Sample3_TruSeq_HiSeqX_rep1; Homo sapiens; Bisulfite-Seq
SRX6640735 Whole Blood 0.781 19.9 61097 954.6 1762 1010.1 3002 10495.8 0.979 GSM3683968: Sample3_TruSeq_HiSeqX_rep2; Homo sapiens; Bisulfite-Seq
SRX6640736 Whole Blood 0.785 46.4 75013 956.8 1655 854.0 3475 12949.6 0.986 GSM3683969: Sample4_Swift_NovaSeq_rep1; Homo sapiens; Bisulfite-Seq
SRX6640737 Whole Blood 0.800 39.3 73655 986.6 1404 854.2 3719 12709.5 0.988 GSM3683970: Sample4_Swift_NovaSeq_rep2; Homo sapiens; Bisulfite-Seq
SRX6640738 Whole Blood 0.635 24.1 63567 868.8 1038 904.2 1674 15622.0 0.992 GSM3683971: Sample4_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640739 Whole Blood 0.791 28.2 71928 949.7 1355 852.2 3884 11717.3 0.986 GSM3683972: Sample4_Swift_HiSeqX_rep1; Homo sapiens; Bisulfite-Seq
SRX6640740 Whole Blood 0.802 22.5 67552 997.7 949 863.1 3957 11445.9 0.988 GSM3683973: Sample4_Swift_HiSeqX_rep2; Homo sapiens; Bisulfite-Seq
SRX6640741 Whole Blood 0.761 25.0 60491 934.3 1548 904.8 1876 13884.1 0.987 GSM3683974: Sample4_TruSeq_HiSeqX_rep1; Homo sapiens; Bisulfite-Seq
SRX6640742 Whole Blood 0.774 15.4 53769 1044.3 896 914.2 1700 16567.2 0.976 GSM3683975: Sample4_TruSeq_HiSeqX_rep2; Homo sapiens; Bisulfite-Seq
SRX6640743 CD4 0.778 22.3 49880 1054.1 765 894.9 2505 10748.9 0.988 GSM3683976: Sample5_Swift_NovaSeq; Homo sapiens; Bisulfite-Seq
SRX6640744 CD4 0.668 9.6 38176 1217.3 192 961.5 1291 13872.8 0.975 GSM3683977: Sample5_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640745 CD4 0.781 25.0 50938 1046.0 817 900.4 2683 10495.5 0.987 GSM3683978: Sample5_Swift_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640746 CD4 0.754 23.5 48301 1012.0 1011 905.5 3240 7846.4 0.989 GSM3683979: Sample5_TruSeq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640747 Neutrophils 0.807 22.7 84372 873.8 775 913.8 4923 10217.3 0.988 GSM3683980: Sample6_Swift_NovaSeq; Homo sapiens; Bisulfite-Seq
SRX6640748 Neutrophils 0.687 10.0 62359 990.8 247 1214.6 2000 15868.2 0.967 GSM3683981: Sample6_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640749 Neutrophils 0.810 27.3 85969 872.5 850 913.3 4213 11700.4 0.987 GSM3683982: Sample6_Swift_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640750 Neutrophils 0.770 23.4 82662 832.1 973 949.0 3982 9679.3 0.989 GSM3683983: Sample6_TruSeq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640751 Neutrophils 0.806 19.6 79275 867.8 1048 1083.5 3568 11745.9 0.989 GSM3683984: Sample7_Swift_NovaSeq; Homo sapiens; Bisulfite-Seq
SRX6640752 Neutrophils 0.697 10.0 59716 976.9 351 1089.2 1679 16588.5 0.973 GSM3683985: Sample7_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640753 Neutrophils 0.809 29.1 81297 880.4 1368 1061.3 4004 12092.0 0.988 GSM3683986: Sample7_Swift_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640754 Neutrophils 0.773 24.3 79595 831.9 1541 1071.3 4271 9333.3 0.990 GSM3683987: Sample7_TruSeq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640755 CD4 0.780 18.0 47550 1092.5 909 1056.0 2285 11411.3 0.988 GSM3683988: Sample8_Swift_NovaSeq; Homo sapiens; Bisulfite-Seq
SRX6640756 CD4 0.665 10.9 40718 1168.3 432 1042.9 1294 14461.4 0.968 GSM3683989: Sample8_QIAseq_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640757 CD4 0.782 22.4 50060 1067.7 1079 1049.7 2932 10399.2 0.987 GSM3683990: Sample8_Swift_HiSeqX; Homo sapiens; Bisulfite-Seq
SRX6640758 CD4 0.754 22.9 48000 1017.6 1603 1052.0 2628 9191.4 0.988 GSM3683991: Sample8_TruSeq_HiSeqX; Homo sapiens; Bisulfite-Seq

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.