Human methylome studies SRP012412 Track Settings
 
GSE59395: Genome-wide map of regulatory interactions in the human genome [A549, Adrenal Gland, Body Of Pancreas, Esophagus Muscularis Mucosa, Esophagus Squamous Epithelium, Fibroblast Of Arm, GM12878, Gastroesophageal Sphincter, HeLa-S3, Heart Left Ventricle, HepG2, Hepatocyte, K562, Lower Leg Skin, Mammary Epithelial Cell, Motor Neuron, OCI-LY7, Ovary, Prostate Gland, Right Lobe Of Liver, SK-N-SH, Smooth Muscle Cell, Spleen, Stomach, Suprapubic Skin, Testis, Thyroid Gland, Tibial Nerve, Transverse Colon, Upper Lobe Of Left Lung]

Track collection: Human methylome studies

+  All tracks in this collection (426)

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experiment
SRX17911857 
SRX17911858 
SRX17911908 
SRX17911909 
SRX17911921 
SRX17911922 
SRX17911952 
SRX17911953 
SRX17911966 
SRX17911967 
SRX17911980 
SRX17911981 
SRX17912009 
SRX17912010 
SRX17912019 
SRX17912020 
SRX17912055 
SRX17912056 
SRX17912092 
SRX17912093 
SRX2156919 
SRX2156920 
SRX2156983 
SRX2156984 
SRX2157007 
SRX2157008 
SRX2157045 
SRX2157046 
SRX2157047 
SRX2157048 
SRX5457071 
SRX5457072 
SRX5457073 
SRX5457074 
SRX5457075 
SRX5457076 
SRX5457077 
SRX5457078 
SRX5457079 
SRX5457080 
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SRX5457083 
SRX5457084 
SRX5457085 
SRX5457086 
SRX5457087 
SRX5457088 
SRX5457089 
SRX5457090 
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SRX5457092 
SRX5457093 
SRX5457094 
SRX5457095 
SRX5457096 
SRX5457097 
SRX5457098 
SRX5457099 
SRX5457100 
SRX5457101 
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SRX5457104 
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SRX5457110 
SRX5457111 
SRX5457112 
SRX5457113 
SRX5457114 
SRX5457115 
SRX5457116 
SRX5457117 
SRX5457118 
SRX5457119 
SRX5457120 
SRX5457121 
experiment
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 SRX17911857  CpG methylation  Motor Neuron / SRX17911857 (CpG methylation)   Data format 
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 SRX17911858  CpG methylation  Motor Neuron / SRX17911858 (CpG methylation)   Data format 
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 SRX17911908  HMR  Motor Neuron / SRX17911908 (HMR)   Data format 
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 SRX17911908  CpG methylation  Motor Neuron / SRX17911908 (CpG methylation)   Data format 
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 SRX17911909  HMR  Motor Neuron / SRX17911909 (HMR)   Data format 
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 SRX17911909  CpG methylation  Motor Neuron / SRX17911909 (CpG methylation)   Data format 
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 SRX17911921  HMR  Motor Neuron / SRX17911921 (HMR)   Data format 
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 SRX17911921  CpG methylation  Motor Neuron / SRX17911921 (CpG methylation)   Data format 
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 SRX17911922  HMR  Motor Neuron / SRX17911922 (HMR)   Data format 
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 SRX17911922  CpG methylation  Motor Neuron / SRX17911922 (CpG methylation)   Data format 
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 SRX17911952  HMR  Motor Neuron / SRX17911952 (HMR)   Data format 
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 SRX17911952  CpG methylation  Motor Neuron / SRX17911952 (CpG methylation)   Data format 
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 SRX17911953  HMR  Motor Neuron / SRX17911953 (HMR)   Data format 
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 SRX17911953  CpG methylation  Motor Neuron / SRX17911953 (CpG methylation)   Data format 
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 SRX17911966  HMR  Motor Neuron / SRX17911966 (HMR)   Data format 
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 SRX17911966  CpG methylation  Motor Neuron / SRX17911966 (CpG methylation)   Data format 
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 SRX17911967  HMR  Motor Neuron / SRX17911967 (HMR)   Data format 
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 SRX17911967  CpG methylation  Motor Neuron / SRX17911967 (CpG methylation)   Data format 
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 SRX17911980  CpG methylation  Motor Neuron / SRX17911980 (CpG methylation)   Data format 
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 SRX17911981  CpG methylation  Motor Neuron / SRX17911981 (CpG methylation)   Data format 
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 SRX17912009  HMR  Motor Neuron / SRX17912009 (HMR)   Data format 
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 SRX17912009  CpG methylation  Motor Neuron / SRX17912009 (CpG methylation)   Data format 
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 SRX17912010  HMR  Motor Neuron / SRX17912010 (HMR)   Data format 
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 SRX17912010  CpG methylation  Motor Neuron / SRX17912010 (CpG methylation)   Data format 
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 SRX17912019  CpG methylation  Motor Neuron / SRX17912019 (CpG methylation)   Data format 
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 SRX17912020  CpG methylation  Motor Neuron / SRX17912020 (CpG methylation)   Data format 
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 SRX17912055  HMR  Motor Neuron / SRX17912055 (HMR)   Data format 
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 SRX17912055  CpG methylation  Motor Neuron / SRX17912055 (CpG methylation)   Data format 
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 SRX17912056  HMR  Motor Neuron / SRX17912056 (HMR)   Data format 
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 SRX17912056  CpG methylation  Motor Neuron / SRX17912056 (CpG methylation)   Data format 
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 SRX17912092  CpG methylation  Motor Neuron / SRX17912092 (CpG methylation)   Data format 
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 SRX17912093  CpG methylation  Motor Neuron / SRX17912093 (CpG methylation)   Data format 
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 SRX2156919  CpG methylation  Fibroblast Of Arm / SRX2156919 (CpG methylation)   Data format 
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 SRX2156920  CpG methylation  Fibroblast Of Arm / SRX2156920 (CpG methylation)   Data format 
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 SRX2156983  HMR  Mammary Epithelial Cell / SRX2156983 (HMR)   Data format 
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 SRX2156983  CpG methylation  Mammary Epithelial Cell / SRX2156983 (CpG methylation)   Data format 
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 SRX2156984  HMR  Mammary Epithelial Cell / SRX2156984 (HMR)   Data format 
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 SRX2156984  CpG methylation  Mammary Epithelial Cell / SRX2156984 (CpG methylation)   Data format 
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 SRX2157007  CpG methylation  K562 / SRX2157007 (CpG methylation)   Data format 
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 SRX2157008  CpG methylation  K562 / SRX2157008 (CpG methylation)   Data format 
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 SRX2157045  CpG methylation  HepG2 / SRX2157045 (CpG methylation)   Data format 
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 SRX2157046  CpG methylation  HepG2 / SRX2157046 (CpG methylation)   Data format 
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 SRX2157047  CpG methylation  GM12878 / SRX2157047 (CpG methylation)   Data format 
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 SRX2157048  CpG methylation  GM12878 / SRX2157048 (CpG methylation)   Data format 
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 SRX5457071  HMR  Testis / SRX5457071 (HMR)   Data format 
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 SRX5457071  CpG methylation  Testis / SRX5457071 (CpG methylation)   Data format 
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 SRX5457072  HMR  Adrenal Gland / SRX5457072 (HMR)   Data format 
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 SRX5457072  CpG methylation  Adrenal Gland / SRX5457072 (CpG methylation)   Data format 
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 SRX5457073  HMR  Smooth Muscle Cell / SRX5457073 (HMR)   Data format 
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 SRX5457073  CpG methylation  Smooth Muscle Cell / SRX5457073 (CpG methylation)   Data format 
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 SRX5457074  HMR  Smooth Muscle Cell / SRX5457074 (HMR)   Data format 
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 SRX5457074  CpG methylation  Smooth Muscle Cell / SRX5457074 (CpG methylation)   Data format 
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 SRX5457075  HMR  Right Lobe Of Liver / SRX5457075 (HMR)   Data format 
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 SRX5457075  CpG methylation  Right Lobe Of Liver / SRX5457075 (CpG methylation)   Data format 
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 SRX5457076  HMR  Right Lobe Of Liver / SRX5457076 (HMR)   Data format 
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 SRX5457076  CpG methylation  Right Lobe Of Liver / SRX5457076 (CpG methylation)   Data format 
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 SRX5457077  HMR  Lower Leg Skin / SRX5457077 (HMR)   Data format 
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 SRX5457077  CpG methylation  Lower Leg Skin / SRX5457077 (CpG methylation)   Data format 
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 SRX5457078  CpG methylation  SK-N-SH / SRX5457078 (CpG methylation)   Data format 
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 SRX5457079  CpG methylation  SK-N-SH / SRX5457079 (CpG methylation)   Data format 
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 SRX5457080  HMR  Transverse Colon / SRX5457080 (HMR)   Data format 
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 SRX5457080  CpG methylation  Transverse Colon / SRX5457080 (CpG methylation)   Data format 
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 SRX5457081  HMR  Suprapubic Skin / SRX5457081 (HMR)   Data format 
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 SRX5457081  CpG methylation  Suprapubic Skin / SRX5457081 (CpG methylation)   Data format 
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 SRX5457082  HMR  Upper Lobe Of Left Lung / SRX5457082 (HMR)   Data format 
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 SRX5457082  CpG methylation  Upper Lobe Of Left Lung / SRX5457082 (CpG methylation)   Data format 
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 SRX5457083  HMR  Stomach / SRX5457083 (HMR)   Data format 
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 SRX5457083  CpG methylation  Stomach / SRX5457083 (CpG methylation)   Data format 
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 SRX5457084  HMR  Ovary / SRX5457084 (HMR)   Data format 
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 SRX5457084  CpG methylation  Ovary / SRX5457084 (CpG methylation)   Data format 
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 SRX5457085  HMR  Heart Left Ventricle / SRX5457085 (HMR)   Data format 
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 SRX5457085  CpG methylation  Heart Left Ventricle / SRX5457085 (CpG methylation)   Data format 
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 SRX5457086  HMR  Body Of Pancreas / SRX5457086 (HMR)   Data format 
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 SRX5457086  CpG methylation  Body Of Pancreas / SRX5457086 (CpG methylation)   Data format 
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 SRX5457087  HMR  Hepatocyte / SRX5457087 (HMR)   Data format 
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 SRX5457087  CpG methylation  Hepatocyte / SRX5457087 (CpG methylation)   Data format 
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 SRX5457088  HMR  Hepatocyte / SRX5457088 (HMR)   Data format 
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 SRX5457088  CpG methylation  Hepatocyte / SRX5457088 (CpG methylation)   Data format 
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 SRX5457089  HMR  Thyroid Gland / SRX5457089 (HMR)   Data format 
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 SRX5457089  CpG methylation  Thyroid Gland / SRX5457089 (CpG methylation)   Data format 
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 SRX5457090  CpG methylation  A549 / SRX5457090 (CpG methylation)   Data format 
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 SRX5457091  CpG methylation  A549 / SRX5457091 (CpG methylation)   Data format 
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 SRX5457092  HMR  Esophagus Squamous Epithelium / SRX5457092 (HMR)   Data format 
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 SRX5457092  CpG methylation  Esophagus Squamous Epithelium / SRX5457092 (CpG methylation)   Data format 
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 SRX5457093  HMR  Gastroesophageal Sphincter / SRX5457093 (HMR)   Data format 
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 SRX5457093  CpG methylation  Gastroesophageal Sphincter / SRX5457093 (CpG methylation)   Data format 
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 SRX5457094  CpG methylation  HeLa-S3 / SRX5457094 (CpG methylation)   Data format 
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 SRX5457095  CpG methylation  HeLa-S3 / SRX5457095 (CpG methylation)   Data format 
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 SRX5457096  HMR  Stomach / SRX5457096 (HMR)   Data format 
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 SRX5457096  CpG methylation  Stomach / SRX5457096 (CpG methylation)   Data format 
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 SRX5457097  HMR  Thyroid Gland / SRX5457097 (HMR)   Data format 
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 SRX5457097  CpG methylation  Thyroid Gland / SRX5457097 (CpG methylation)   Data format 
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 SRX5457098  CpG methylation  Fibroblast Of Arm / SRX5457098 (CpG methylation)   Data format 
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 SRX5457099  CpG methylation  Fibroblast Of Arm / SRX5457099 (CpG methylation)   Data format 
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 SRX5457100  HMR  Tibial Nerve / SRX5457100 (HMR)   Data format 
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 SRX5457100  CpG methylation  Tibial Nerve / SRX5457100 (CpG methylation)   Data format 
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 SRX5457101  HMR  Transverse Colon / SRX5457101 (HMR)   Data format 
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 SRX5457101  CpG methylation  Transverse Colon / SRX5457101 (CpG methylation)   Data format 
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 SRX5457102  HMR  Upper Lobe Of Left Lung / SRX5457102 (HMR)   Data format 
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 SRX5457102  CpG methylation  Upper Lobe Of Left Lung / SRX5457102 (CpG methylation)   Data format 
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 SRX5457103  HMR  Adrenal Gland / SRX5457103 (HMR)   Data format 
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 SRX5457103  CpG methylation  Adrenal Gland / SRX5457103 (CpG methylation)   Data format 
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 SRX5457104  HMR  Spleen / SRX5457104 (HMR)   Data format 
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 SRX5457104  CpG methylation  Spleen / SRX5457104 (CpG methylation)   Data format 
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 SRX5457105  HMR  Tibial Nerve / SRX5457105 (HMR)   Data format 
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 SRX5457105  CpG methylation  Tibial Nerve / SRX5457105 (CpG methylation)   Data format 
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 SRX5457106  HMR  Spleen / SRX5457106 (HMR)   Data format 
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 SRX5457106  CpG methylation  Spleen / SRX5457106 (CpG methylation)   Data format 
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 SRX5457107  HMR  Heart Left Ventricle / SRX5457107 (HMR)   Data format 
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 SRX5457107  CpG methylation  Heart Left Ventricle / SRX5457107 (CpG methylation)   Data format 
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 SRX5457108  HMR  Prostate Gland / SRX5457108 (HMR)   Data format 
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 SRX5457108  CpG methylation  Prostate Gland / SRX5457108 (CpG methylation)   Data format 
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 SRX5457109  CpG methylation  HepG2 / SRX5457109 (CpG methylation)   Data format 
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 SRX5457110  CpG methylation  HepG2 / SRX5457110 (CpG methylation)   Data format 
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 SRX5457111  HMR  Ovary / SRX5457111 (HMR)   Data format 
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 SRX5457111  CpG methylation  Ovary / SRX5457111 (CpG methylation)   Data format 
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 SRX5457112  HMR  Testis / SRX5457112 (HMR)   Data format 
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 SRX5457112  CpG methylation  Testis / SRX5457112 (CpG methylation)   Data format 
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 SRX5457113  HMR  Gastroesophageal Sphincter / SRX5457113 (HMR)   Data format 
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 SRX5457113  CpG methylation  Gastroesophageal Sphincter / SRX5457113 (CpG methylation)   Data format 
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 SRX5457114  HMR  Esophagus Squamous Epithelium / SRX5457114 (HMR)   Data format 
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 SRX5457114  CpG methylation  Esophagus Squamous Epithelium / SRX5457114 (CpG methylation)   Data format 
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 SRX5457115  HMR  Esophagus Muscularis Mucosa / SRX5457115 (HMR)   Data format 
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 SRX5457115  CpG methylation  Esophagus Muscularis Mucosa / SRX5457115 (CpG methylation)   Data format 
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 SRX5457116  HMR  Lower Leg Skin / SRX5457116 (HMR)   Data format 
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 SRX5457116  CpG methylation  Lower Leg Skin / SRX5457116 (CpG methylation)   Data format 
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 SRX5457117  HMR  Smooth Muscle Cell / SRX5457117 (HMR)   Data format 
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 SRX5457117  CpG methylation  Smooth Muscle Cell / SRX5457117 (CpG methylation)   Data format 
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 SRX5457118  HMR  Smooth Muscle Cell / SRX5457118 (HMR)   Data format 
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 SRX5457118  CpG methylation  Smooth Muscle Cell / SRX5457118 (CpG methylation)   Data format 
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 SRX5457119  HMR  Body Of Pancreas / SRX5457119 (HMR)   Data format 
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 SRX5457119  CpG methylation  Body Of Pancreas / SRX5457119 (CpG methylation)   Data format 
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 SRX5457120  HMR  OCI-LY7 / SRX5457120 (HMR)   Data format 
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 SRX5457120  CpG methylation  OCI-LY7 / SRX5457120 (CpG methylation)   Data format 
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 SRX5457121  HMR  OCI-LY7 / SRX5457121 (HMR)   Data format 
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 SRX5457121  CpG methylation  OCI-LY7 / SRX5457121 (CpG methylation)   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

Study title: GSE59395: Genome-wide map of regulatory interactions in the human genome
SRA: SRP012412
GEO: GSE59395
Pubmed: 25228660

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Title
SRX17911857 Motor Neuron 0.576 10.6 65409 10378.5 49 1270.4 2468 435174.5 0.992 GSM6637750: WGBS from motor neuron (ENCLB545KAC); Homo sapiens; Bisulfite-Seq
SRX17911858 Motor Neuron 0.576 9.9 63442 10626.8 49 1073.2 2464 434308.6 0.992 GSM6637751: WGBS from motor neuron (ENCLB128RQU); Homo sapiens; Bisulfite-Seq
SRX17911908 Motor Neuron 0.801 6.0 40075 2140.6 42 1033.9 1574 100428.9 0.986 GSM6637801: WGBS from motor neuron (ENCLB512EKL); Homo sapiens; Bisulfite-Seq
SRX17911909 Motor Neuron 0.812 8.7 44195 2068.3 65 1087.5 1617 102859.1 0.983 GSM6637802: WGBS from motor neuron (ENCLB467MJJ); Homo sapiens; Bisulfite-Seq
SRX17911921 Motor Neuron 0.773 3.3 32800 2668.9 18 1384.9 939 183059.7 0.989 GSM6637832: WGBS from motor neuron (ENCLB911ZVW); Homo sapiens; Bisulfite-Seq
SRX17911922 Motor Neuron 0.768 5.8 41347 2243.3 35 1175.5 1264 130053.7 0.991 GSM6637833: WGBS from motor neuron (ENCLB805ZXC); Homo sapiens; Bisulfite-Seq
SRX17911952 Motor Neuron 0.757 2.7 26798 2231.3 32 1137.6 743 231265.0 0.981 GSM6637873: WGBS from motor neuron (ENCLB903FBM); Homo sapiens; Bisulfite-Seq
SRX17911953 Motor Neuron 0.788 7.5 37263 1896.8 38 1150.0 1656 91483.8 0.991 GSM6637874: WGBS from motor neuron (ENCLB266MMU); Homo sapiens; Bisulfite-Seq
SRX17911966 Motor Neuron 0.776 6.7 38772 2874.8 29 1181.4 1367 180250.7 0.990 GSM6637895: WGBS from motor neuron (ENCLB771WTH); Homo sapiens; Bisulfite-Seq
SRX17911967 Motor Neuron 0.777 6.0 38399 2873.1 25 1128.6 1290 189769.2 0.987 GSM6637896: WGBS from motor neuron (ENCLB789HCY); Homo sapiens; Bisulfite-Seq
SRX17911980 Motor Neuron 0.530 9.0 59522 12136.9 161 992.2 2346 440730.5 0.991 GSM6637915: WGBS from motor neuron (ENCLB387VFA); Homo sapiens; Bisulfite-Seq
SRX17911981 Motor Neuron 0.532 8.2 56256 12753.2 150 1003.2 2315 440740.4 0.991 GSM6637916: WGBS from motor neuron (ENCLB252YID); Homo sapiens; Bisulfite-Seq
SRX17912009 Motor Neuron 0.792 13.8 53859 1894.3 139 1122.2 2673 59586.5 0.991 GSM6637962: WGBS from motor neuron (ENCLB567IQG); Homo sapiens; Bisulfite-Seq
SRX17912010 Motor Neuron 0.789 13.2 53387 1872.3 155 1098.8 2480 63087.1 0.991 GSM6637963: WGBS from motor neuron (ENCLB229KTN); Homo sapiens; Bisulfite-Seq
SRX17912019 Motor Neuron 0.539 10.5 72539 11028.9 127 946.6 2947 377388.0 0.992 GSM6638026: WGBS from motor neuron (ENCLB677ZQW); Homo sapiens; Bisulfite-Seq
SRX17912020 Motor Neuron 0.531 9.6 63897 12353.2 87 1000.9 2885 384938.4 0.991 GSM6638027: WGBS from motor neuron (ENCLB396TQW); Homo sapiens; Bisulfite-Seq
SRX17912055 Motor Neuron 0.779 13.4 53400 2573.8 243 1129.8 2030 124392.1 0.991 GSM6638060: WGBS from motor neuron (ENCLB201YCD); Homo sapiens; Bisulfite-Seq
SRX17912056 Motor Neuron 0.775 11.7 51938 2551.1 211 1096.0 2028 123753.4 0.991 GSM6638061: WGBS from motor neuron (ENCLB602ZNP); Homo sapiens; Bisulfite-Seq
SRX17912092 Motor Neuron 0.611 9.5 61918 8432.9 56 1108.2 2504 384715.0 0.991 GSM6638098: WGBS from motor neuron (ENCLB433QRA); Homo sapiens; Bisulfite-Seq
SRX17912093 Motor Neuron 0.610 10.4 62792 8245.8 59 1062.6 2534 381353.2 0.991 GSM6638099: WGBS from motor neuron (ENCLB183KKE); Homo sapiens; Bisulfite-Seq
SRX2156919 Fibroblast Of Arm 0.601 23.4 85025 9739.6 584 923.2 3476 325776.7 0.989 GSM2308512: WGBS from fibroblast of arm (ENCLB091KWS); Homo sapiens; Bisulfite-Seq
SRX2156920 Fibroblast Of Arm 0.602 27.0 87689 9548.3 702 922.2 3480 326414.4 0.988 GSM2308513: WGBS from fibroblast of arm (ENCLB373TCH); Homo sapiens; Bisulfite-Seq
SRX2156983 Mammary Epithelial Cell 0.709 19.7 72120 2982.7 1174 1044.3 2123 503683.7 0.984 GSM2308566: WGBS from mammary epithelial cell (ENCLB975DHQ); Homo sapiens; Bisulfite-Seq
SRX2156984 Mammary Epithelial Cell 0.710 16.9 68994 2997.9 862 1081.0 2099 509263.1 0.984 GSM2308567: WGBS from mammary epithelial cell (ENCLB522AUR); Homo sapiens; Bisulfite-Seq
SRX2157007 K562 0.263 25.1 130854 13397.0 1881 1139.0 8554 200282.9 0.994 GSM2308596: WGBS from K562 (ENCLB542OXH); Homo sapiens; Bisulfite-Seq
SRX2157008 K562 0.266 24.2 135024 12922.6 1820 1030.5 8914 189570.8 0.994 GSM2308597: WGBS from K562 (ENCLB742NWU); Homo sapiens; Bisulfite-Seq
SRX2157045 HepG2 0.432 13.3 53673 17046.9 646 1059.5 2363 763850.7 0.994 GSM2308630: WGBS from HepG2 (ENCLB569VMN); Homo sapiens; Bisulfite-Seq
SRX2157046 HepG2 0.443 26.7 113066 10196.7 1398 1074.4 2542 723933.1 0.994 GSM2308631: WGBS from HepG2 (ENCLB223EJM); Homo sapiens; Bisulfite-Seq
SRX2157047 GM12878 0.477 21.4 76501 9194.7 2626 1104.5 1705 987783.4 0.992 GSM2308632: WGBS from GM12878 (ENCLB794YYH); Homo sapiens; Bisulfite-Seq
SRX2157048 GM12878 0.518 26.7 56638 12572.4 1312 1076.2 1720 992706.0 0.993 GSM2308633: WGBS from GM12878 (ENCLB898WPW); Homo sapiens; Bisulfite-Seq
SRX5457071 Testis 0.767 19.0 38793 1330.3 22184 993.3 3649 24723.1 0.992 GSM3633629: WGBS from testis (ENCLB904LWN); Homo sapiens; Bisulfite-Seq
SRX5457072 Adrenal Gland 0.744 26.6 43209 1089.8 1579 919.9 2428 14365.1 0.992 GSM3633630: WGBS from adrenal gland (ENCLB206OWW); Homo sapiens; Bisulfite-Seq
SRX5457073 Smooth Muscle Cell 0.810 31.9 63029 1084.9 1235 1189.4 3825 30784.9 0.993 GSM3633631: WGBS from smooth muscle cell (ENCLB753MSX); Homo sapiens; Bisulfite-Seq
SRX5457074 Smooth Muscle Cell 0.813 29.1 62512 1066.8 1020 1239.4 4030 29275.2 0.993 GSM3633632: WGBS from smooth muscle cell (ENCLB101NNR); Homo sapiens; Bisulfite-Seq
SRX5457075 Right Lobe Of Liver 0.716 12.7 35297 1376.5 551 878.5 5187 117929.1 0.993 GSM3633633: WGBS from right lobe of liver (ENCLB516XAY); Homo sapiens; Bisulfite-Seq
SRX5457076 Right Lobe Of Liver 0.719 21.8 38492 1242.4 3092 976.9 4331 167414.5 0.994 GSM3633634: WGBS from right lobe of liver (ENCLB061REQ); Homo sapiens; Bisulfite-Seq
SRX5457077 Lower Leg Skin 0.788 29.1 55516 1149.1 3599 924.3 3265 13927.6 0.994 GSM3633635: WGBS from lower leg skin (ENCLB672LGT); Homo sapiens; Bisulfite-Seq
SRX5457078 SK-N-SH 0.581 28.7 81046 11757.1 3656 1425.6 2428 541249.3 0.994 GSM3633636: WGBS from SK-N-SH (ENCLB406PIZ); Homo sapiens; Bisulfite-Seq
SRX5457079 SK-N-SH 0.580 30.0 77405 12317.7 3457 1285.6 2519 521344.3 0.994 GSM3633637: WGBS from SK-N-SH (ENCLB721ONH); Homo sapiens; Bisulfite-Seq
SRX5457080 Transverse Colon 0.742 7.8 34504 1413.0 232 874.8 1205 18035.4 0.992 GSM3633680: WGBS from transverse colon (ENCLB704GVM); Homo sapiens; Bisulfite-Seq
SRX5457081 Suprapubic Skin 0.783 24.9 50166 1121.5 2776 944.8 3203 11072.6 0.994 GSM3633681: WGBS from suprapubic skin (ENCLB852KRZ); Homo sapiens; Bisulfite-Seq
SRX5457082 Upper Lobe Of Left Lung 0.796 25.6 45023 1144.0 1160 916.5 2842 15494.2 0.993 GSM3633682: WGBS from upper lobe of left lung (ENCLB937HGI); Homo sapiens; Bisulfite-Seq
SRX5457083 Stomach 0.751 22.6 43669 1144.5 2624 921.6 2740 12555.9 0.994 GSM3633683: WGBS from stomach (ENCLB658ATV); Homo sapiens; Bisulfite-Seq
SRX5457084 Ovary 0.765 32.6 82752 1123.8 1046 1126.2 3011 13555.2 0.994 GSM3633684: WGBS from ovary (ENCLB858YYV); Homo sapiens; Bisulfite-Seq
SRX5457085 Heart Left Ventricle 0.756 31.0 50831 1081.3 2866 962.1 3601 19877.3 0.992 GSM3633685: WGBS from heart left ventricle (ENCLB439FZB); Homo sapiens; Bisulfite-Seq
SRX5457086 Body Of Pancreas 0.719 23.7 47652 1278.0 938 980.2 3172 27956.1 0.992 GSM3633686: WGBS from body of pancreas (ENCLB777VZI); Homo sapiens; Bisulfite-Seq
SRX5457087 Hepatocyte 0.796 33.2 55703 1241.6 2358 1029.0 3456 35358.5 0.988 GSM3633801: WGBS from hepatocyte (ENCLB409PWJ); Homo sapiens; Bisulfite-Seq
SRX5457088 Hepatocyte 0.798 30.9 54379 1222.4 2151 1054.8 3554 34069.2 0.986 GSM3633803: WGBS from hepatocyte (ENCLB757MBA); Homo sapiens; Bisulfite-Seq
SRX5457089 Thyroid Gland 0.820 35.1 60387 1133.7 1112 850.2 3245 19666.0 0.993 GSM3633921: WGBS from thyroid gland (ENCLB955VCW); Homo sapiens; Bisulfite-Seq
SRX5457090 A549 0.558 31.9 107411 8625.0 542 959.1 3076 392732.6 0.994 GSM3633943: WGBS from A549 (ENCLB094KJP); Homo sapiens; Bisulfite-Seq
SRX5457091 A549 0.559 33.0 107784 8583.2 578 943.6 3104 391029.4 0.994 GSM3633944: WGBS from A549 (ENCLB456FMY); Homo sapiens; Bisulfite-Seq
SRX5457092 Esophagus Squamous Epithelium 0.749 16.8 39441 1183.8 1366 945.8 2340 11364.1 0.994 GSM3633945: WGBS from esophagus squamous epithelium (ENCLB186SWN); Homo sapiens; Bisulfite-Seq
SRX5457093 Gastroesophageal Sphincter 0.757 13.2 44133 1230.2 236 952.9 2706 13913.4 0.993 GSM3633946: WGBS from gastroesophageal sphincter (ENCLB201VYW); Homo sapiens; Bisulfite-Seq
SRX5457094 HeLa-S3 0.602 24.8 109414 8657.8 1136 923.8 3722 324385.1 0.994 GSM3633947: WGBS from HeLa-S3 (ENCLB145KPM); Homo sapiens; Bisulfite-Seq
SRX5457095 HeLa-S3 0.613 36.6 121495 7959.3 1863 929.4 3757 324349.0 0.995 GSM3633948: WGBS from HeLa-S3 (ENCLB756LAB); Homo sapiens; Bisulfite-Seq
SRX5457096 Stomach 0.769 24.8 49246 1150.1 2688 972.4 3048 13174.4 0.994 GSM3633949: WGBS from stomach (ENCLB479ACS); Homo sapiens; Bisulfite-Seq
SRX5457097 Thyroid Gland 0.811 31.5 53827 1101.5 1475 857.9 3119 15899.4 0.993 GSM3633950: WGBS from thyroid gland (ENCLB295YNJ); Homo sapiens; Bisulfite-Seq
SRX5457098 Fibroblast Of Arm 0.606 31.5 91403 9164.6 774 904.8 3529 320300.2 0.994 GSM3633951: WGBS from GM23248 (ENCLB436YZI); Homo sapiens; Bisulfite-Seq
SRX5457099 Fibroblast Of Arm 0.605 38.8 92837 9076.3 868 932.5 3487 324001.4 0.994 GSM3633952: WGBS from GM23248 (ENCLB777FMV); Homo sapiens; Bisulfite-Seq
SRX5457100 Tibial Nerve 0.788 25.1 56447 1120.5 1602 943.8 3288 13311.3 0.994 GSM3633953: WGBS from tibial nerve (ENCLB655QZP); Homo sapiens; Bisulfite-Seq
SRX5457101 Transverse Colon 0.762 29.0 43717 1154.1 4510 1017.9 2678 10625.1 0.993 GSM3633954: WGBS from transverse colon (ENCLB373KCT); Homo sapiens; Bisulfite-Seq
SRX5457102 Upper Lobe Of Left Lung 0.776 24.9 47497 1102.2 3049 946.6 3070 13392.6 0.993 GSM3633955: WGBS from upper lobe of left lung (ENCLB271HNF); Homo sapiens; Bisulfite-Seq
SRX5457103 Adrenal Gland 0.770 22.3 42304 1102.6 1535 975.6 2944 13653.1 0.992 GSM3633956: WGBS from adrenal gland (ENCLB543VBP); Homo sapiens; Bisulfite-Seq
SRX5457104 Spleen 0.771 29.4 44798 1073.8 2175 987.4 2890 11839.4 0.994 GSM3633957: WGBS from spleen (ENCLB845KXJ); Homo sapiens; Bisulfite-Seq
SRX5457105 Tibial Nerve 0.782 31.1 55830 1122.0 2531 991.9 3036 12705.4 0.994 GSM3633958: WGBS from tibial nerve (ENCLB901CGI); Homo sapiens; Bisulfite-Seq
SRX5457106 Spleen 0.797 26.6 52121 1038.5 1088 871.0 3361 12664.5 0.994 GSM3633974: WGBS from spleen (ENCLB353RJB); Homo sapiens; Bisulfite-Seq
SRX5457107 Heart Left Ventricle 0.755 29.6 49146 1089.0 2943 977.6 2780 20932.4 0.993 GSM3633975: WGBS from heart left ventricle (ENCLB560LZP); Homo sapiens; Bisulfite-Seq
SRX5457108 Prostate Gland 0.773 27.4 68097 1163.7 2265 899.7 2956 12687.0 0.994 GSM3633976: WGBS from prostate gland (ENCLB428IRX); Homo sapiens; Bisulfite-Seq
SRX5457109 HepG2 0.450 25.3 78994 13380.7 713 989.8 2383 760468.6 0.993 GSM3633977: WGBS from HepG2 (ENCLB890RFU); Homo sapiens; Bisulfite-Seq
SRX5457110 HepG2 0.453 30.5 99139 11287.0 920 1010.5 2379 762812.0 0.994 GSM3633978: WGBS from HepG2 (ENCLB443JJF); Homo sapiens; Bisulfite-Seq
SRX5457111 Ovary 0.784 34.5 73315 1168.8 1337 1055.2 3126 14219.2 0.994 GSM3633985: WGBS from ovary (ENCLB056RXQ); Homo sapiens; Bisulfite-Seq
SRX5457112 Testis 0.776 30.0 52837 1330.3 14744 972.2 3660 24879.4 0.993 GSM3633986: WGBS from testis (ENCLB095PBB); Homo sapiens; Bisulfite-Seq
SRX5457113 Gastroesophageal Sphincter 0.756 8.5 40225 1310.0 131 989.3 3009 11923.0 0.993 GSM3633989: WGBS from gastroesophageal sphincter (ENCLB515SVA); Homo sapiens; Bisulfite-Seq
SRX5457114 Esophagus Squamous Epithelium 0.742 18.8 44571 1196.2 1373 872.8 2223 12724.0 0.994 GSM3633990: WGBS from esophagus squamous epithelium (ENCLB776RBC); Homo sapiens; Bisulfite-Seq
SRX5457115 Esophagus Muscularis Mucosa 0.776 22.2 46638 1141.8 1328 1006.3 2895 17096.6 0.993 GSM3633991: WGBS from esophagus muscularis mucosa (ENCLB195SCD); Homo sapiens; Bisulfite-Seq
SRX5457116 Lower Leg Skin 0.778 26.9 53173 1131.3 4287 983.5 2944 12542.7 0.994 GSM3633992: WGBS from lower leg skin (ENCLB460MSR); Homo sapiens; Bisulfite-Seq
SRX5457117 Smooth Muscle Cell 0.805 36.1 67680 1216.5 1502 1173.8 3927 34849.8 0.990 GSM3633993: WGBS from smooth muscle cell (ENCLB767YYU); Homo sapiens; Bisulfite-Seq
SRX5457118 Smooth Muscle Cell 0.809 33.4 66086 1211.7 1567 1162.7 4132 33442.6 0.990 GSM3633994: WGBS from smooth muscle cell (ENCLB125PJJ); Homo sapiens; Bisulfite-Seq
SRX5457119 Body Of Pancreas 0.722 28.2 50125 1192.0 1985 1003.0 3430 25906.1 0.993 GSM3633995: WGBS from body of pancreas (ENCLB417QPU); Homo sapiens; Bisulfite-Seq
SRX5457120 OCI-LY7 0.642 36.7 85133 2339.6 3518 1041.1 893 1367756.1 0.994 GSM3634061: WGBS from OCI-LY7 (ENCLB588PCW); Homo sapiens; Bisulfite-Seq
SRX5457121 OCI-LY7 0.640 32.3 79039 2434.0 2781 1021.0 846 1402925.0 0.995 GSM3634062: WGBS from OCI-LY7 (ENCLB172JDR); 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.