Human methylome studies SRP012412 Track Settings
Study title: GSE59395: Genome-wide map of regulatory interactions in the human genomeSRA: SRP012412 GEO: GSE59395 Pubmed: 25228660
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
SRX17911857 Motor Neuron
0.576
10.6
65409
10378.5
49
1270.4
2468
435174.5
0.992
title: GSM6637750 WGBS from motor neuron (ENCLB545KAC), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "49 year", "donor_ID": "ENCDO272LDF", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911858 Motor Neuron
0.576
9.9
63442
10626.8
49
1073.2
2464
434308.6
0.992
title: GSM6637751 WGBS from motor neuron (ENCLB128RQU), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "49 year", "donor_ID": "ENCDO272LDF", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911908 Motor Neuron
0.801
6.0
40075
2140.6
42
1033.9
1574
100428.9
0.986
title: GSM6637801 WGBS from motor neuron (ENCLB512EKL), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male child (6 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "child", "age": "6 year", "donor_ID": "ENCDO022IAQ", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911909 Motor Neuron
0.812
8.7
44195
2068.3
65
1087.5
1617
102859.1
0.983
title: GSM6637802 WGBS from motor neuron (ENCLB467MJJ), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male child (6 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "child", "age": "6 year", "donor_ID": "ENCDO022IAQ", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911921 Motor Neuron
0.773
3.3
32800
2668.9
18
1384.9
939
183059.7
0.989
title: GSM6637832 WGBS from motor neuron (ENCLB911ZVW), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens female adult motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "female", "health_state": "Healthy donor", "dev_stage": "adult", "age": "not collected", "donor_ID": "ENCDO689YDN", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911922 Motor Neuron
0.768
5.8
41347
2243.3
35
1175.5
1264
130053.7
0.991
title: GSM6637833 WGBS from motor neuron (ENCLB805ZXC), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens female adult motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "female", "health_state": "Healthy donor", "dev_stage": "adult", "age": "not collected", "donor_ID": "ENCDO689YDN", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911952 Motor Neuron
0.757
2.7
26798
2231.3
32
1137.6
743
231265.0
0.981
title: GSM6637873 WGBS from motor neuron (ENCLB903FBM), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens female adult motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "female", "health_state": "Healthy donor", "dev_stage": "adult", "age": "not collected", "donor_ID": "ENCDO689YDN", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911953 Motor Neuron
0.788
7.5
37263
1896.8
38
1150.0
1656
91483.8
0.991
title: GSM6637874 WGBS from motor neuron (ENCLB266MMU), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens female adult motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "female", "health_state": "Healthy donor", "dev_stage": "adult", "age": "not collected", "donor_ID": "ENCDO689YDN", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911966 Motor Neuron
0.776
6.7
38772
2874.8
29
1181.4
1367
180250.7
0.990
title: GSM6637895 WGBS from motor neuron (ENCLB771WTH), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male child (6 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "child", "age": "6 year", "donor_ID": "ENCDO022IAQ", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911967 Motor Neuron
0.777
6.0
38399
2873.1
25
1128.6
1290
189769.2
0.987
title: GSM6637896 WGBS from motor neuron (ENCLB789HCY), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male child (6 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "child", "age": "6 year", "donor_ID": "ENCDO022IAQ", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911980 Motor Neuron
0.530
9.0
59522
12136.9
161
992.2
2346
440730.5
0.991
title: GSM6637915 WGBS from motor neuron (ENCLB387VFA), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "47 year", "donor_ID": "ENCDO565NIZ", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17911981 Motor Neuron
0.532
8.2
56256
12753.2
150
1003.2
2315
440740.4
0.991
title: GSM6637916 WGBS from motor neuron (ENCLB252YID), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "47 year", "donor_ID": "ENCDO565NIZ", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912009 Motor Neuron
0.792
13.8
53859
1894.3
139
1122.2
2673
59586.5
0.991
title: GSM6637962 WGBS from motor neuron (ENCLB567IQG), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "49 year", "donor_ID": "ENCDO272LDF", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912010 Motor Neuron
0.789
13.2
53387
1872.3
155
1098.8
2480
63087.1
0.991
title: GSM6637963 WGBS from motor neuron (ENCLB229KTN), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "49 year", "donor_ID": "ENCDO272LDF", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912019 Motor Neuron
0.539
10.5
72539
11028.9
127
946.6
2947
377388.0
0.992
title: GSM6638026 WGBS from motor neuron (ENCLB677ZQW), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "47 year", "donor_ID": "ENCDO908CUN", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912020 Motor Neuron
0.531
9.6
63897
12353.2
87
1000.9
2885
384938.4
0.991
title: GSM6638027 WGBS from motor neuron (ENCLB396TQW), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Donor with Amyotrophic Lateral Sclerosis", "dev_stage": "adult", "age": "47 year", "donor_ID": "ENCDO908CUN", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912055 Motor Neuron
0.779
13.4
53400
2573.8
243
1129.8
2030
124392.1
0.991
title: GSM6638060 WGBS from motor neuron (ENCLB201YCD), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "adult", "age": "55 year", "donor_ID": "ENCDO371BAE", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912056 Motor Neuron
0.775
11.7
51938
2551.1
211
1096.0
2028
123753.4
0.991
title: GSM6638061 WGBS from motor neuron (ENCLB602ZNP), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "adult", "age": "55 year", "donor_ID": "ENCDO371BAE", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912092 Motor Neuron
0.611
9.5
61918
8432.9
56
1108.2
2504
384715.0
0.991
title: GSM6638098 WGBS from motor neuron (ENCLB433QRA), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "adult", "age": "55 year", "donor_ID": "ENCDO371BAE", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX17912093 Motor Neuron
0.610
10.4
62792
8245.8
59
1062.6
2534
381353.2
0.991
title: GSM6638099 WGBS from motor neuron (ENCLB183KKE), Homo sapiens, Bisulfite-Seq; {"description": "Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells", "sample_type": "in vitro differentiated cells", "cell_type": "motor neuron", "sex": "male", "health_state": "Healthy donor", "dev_stage": "adult", "age": "55 year", "donor_ID": "ENCDO371BAE", "lab": "Michael Snyder, Stanford", "source": "Cooper-Knock lab, University of Sheffield, UK"}
SRX2156919 Fibroblast Of Arm
0.601
23.4
85025
9739.6
584
923.2
3476
325776.7
0.989
title: GSM2308512 WGBS from fibroblast of arm (ENCLB091KWS), Homo sapiens, Bisulfite-Seq; {"age": "53 year", "donor_ID": "ENCDO336AAA", "dev_stage": "adult", "sample_type": "primary cell", "cell_type": "fibroblast of arm", "sex": "male", "lab": "Thomas Gingeras, CSHL"}
SRX2156920 Fibroblast Of Arm
0.602
27.0
87689
9548.3
702
922.2
3480
326414.4
0.988
title: GSM2308513 WGBS from fibroblast of arm (ENCLB373TCH), Homo sapiens, Bisulfite-Seq; {"age": "53 year", "donor_ID": "ENCDO336AAA", "dev_stage": "adult", "sample_type": "primary cell", "cell_type": "fibroblast of arm", "sex": "male", "lab": "Thomas Gingeras, CSHL"}
SRX2156983 Mammary Epithelial
0.709
19.7
72120
2982.7
1174
1044.3
2123
503683.7
0.984
title: GSM2308566 WGBS from mammary epithelial cell (ENCLB975DHQ), Homo sapiens, Bisulfite-Seq; {"age": "unknown", "dev_stage": "unknown", "donor_ID": "ENCDO344AAA", "cell_type": "mammary epithelial cell", "sex": "female", "health_state": "unknown", "sample_type": "primary cell", "lab": "Richard Myers, HAIB"}
SRX2156984 Mammary Epithelial
0.710
16.9
68994
2997.9
862
1081.0
2099
509263.1
0.984
title: GSM2308567 WGBS from mammary epithelial cell (ENCLB522AUR), Homo sapiens, Bisulfite-Seq; {"age": "50 year", "dev_stage": "unknown", "donor_ID": "ENCDO830BUW", "cell_type": "mammary epithelial cell", "sex": "female", "sample_type": "primary cell", "lab": "Bradley Bernstein, Broad"}
SRX2157007 Cell Line
0.263
25.1
130854
13397.0
1881
1139.0
8554
200282.9
0.994
title: GSM2308596 WGBS from K562 (ENCLB542OXH), Homo sapiens, Bisulfite-Seq; {"age": "53 year", "dev_stage": "adult", "donor_ID": "ENCDO000AAD", "sex": "female", "health_state": "chronic myelogenous leukemia (CML)", "sample_type": "immortalized cell line", "cell_line": "K562", "passage_number": "6", "lab": "Richard Myers, HAIB"}
SRX2157008 Cell Line
0.266
24.2
135024
12922.6
1820
1030.5
8914
189570.8
0.994
title: GSM2308597 WGBS from K562 (ENCLB742NWU), Homo sapiens, Bisulfite-Seq; {"age": "53 year", "dev_stage": "adult", "donor_ID": "ENCDO000AAD", "sex": "female", "health_state": "chronic myelogenous leukemia (CML)", "sample_type": "immortalized cell line", "cell_line": "K562", "passage_number": "6", "lab": "Richard Myers, HAIB"}
SRX2157045 Cell Line
0.432
13.3
53673
17046.9
646
1059.5
2363
763850.7
0.994
title: GSM2308630 WGBS from HepG2 (ENCLB569VMN), Homo sapiens, Bisulfite-Seq; {"age": "15 year", "dev_stage": "child", "donor_ID": "ENCDO000AAC", "sex": "male", "health_state": "hepatocellular carcinoma", "sample_type": "immortalized cell line", "cell_line": "HepG2", "lab": "Richard Myers, HAIB"}
SRX2157046 Cell Line
0.443
26.7
113066
10196.7
1398
1074.4
2542
723933.1
0.994
title: GSM2308631 WGBS from HepG2 (ENCLB223EJM), Homo sapiens, Bisulfite-Seq; {"age": "15 year", "dev_stage": "child", "donor_ID": "ENCDO000AAC", "sex": "male", "health_state": "hepatocellular carcinoma", "sample_type": "immortalized cell line", "cell_line": "HepG2", "lab": "Richard Myers, HAIB"}
SRX2157047 Cell Line
0.477
21.4
76501
9194.7
2626
1104.5
1705
987783.4
0.992
title: GSM2308632 WGBS from GM12878 (ENCLB794YYH), Homo sapiens, Bisulfite-Seq; {"age": "unknown", "dev_stage": "adult", "donor_ID": "ENCDO000AAK", "sex": "female", "health_state": "unknown", "sample_type": "immortalized cell line", "cell_line": "GM12878", "passage_number": "6", "lab": "Richard Myers, HAIB"}
SRX2157048 Cell Line
0.518
26.7
56638
12572.4
1312
1076.2
1720
992706.0
0.993
title: GSM2308633 WGBS from GM12878 (ENCLB898WPW), Homo sapiens, Bisulfite-Seq; {"age": "unknown", "dev_stage": "adult", "donor_ID": "ENCDO000AAK", "sex": "female", "health_state": "unknown", "sample_type": "immortalized cell line", "cell_line": "GM12878", "passage_number": "16", "lab": "Richard Myers, HAIB"}
SRX5457071 Testis
0.767
19.0
38793
1330.3
22184
993.3
3649
24723.1
0.992
title: GSM3633629 WGBS from testis (ENCLB904LWN), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "testis", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457072 Adrenal Gland
0.744
26.6
43209
1089.8
1579
919.9
2428
14365.1
0.992
title: GSM3633630 WGBS from adrenal gland (ENCLB206OWW), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "adrenal gland", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457073 Smooth Muscle
0.810
31.9
63029
1084.9
1235
1189.4
3825
30784.9
0.993
title: GSM3633631 WGBS from smooth muscle cell (ENCLB753MSX), Homo sapiens, Bisulfite-Seq; {"sample_type": "in vitro differentiated cells", "sex": "female", "health_state": "healthy", "dev_stage": "embryonic", "age": "5 day", "donor_ID": "ENCDO222AAA", "lab": "Richard Myers, HAIB", "cell_type": "smooth muscle cell"}
SRX5457074 Smooth Muscle
0.813
29.1
62512
1066.8
1020
1239.4
4030
29275.2
0.993
title: GSM3633632 WGBS from smooth muscle cell (ENCLB101NNR), Homo sapiens, Bisulfite-Seq; {"sample_type": "in vitro differentiated cells", "sex": "female", "health_state": "healthy", "dev_stage": "embryonic", "age": "5 day", "donor_ID": "ENCDO222AAA", "lab": "Richard Myers, HAIB", "cell_type": "smooth muscle cell"}
SRX5457075 Right Lobe Of Liver
0.716
12.7
35297
1376.5
551
878.5
5187
117929.1
0.993
title: GSM3633633 WGBS from right lobe of liver (ENCLB516XAY), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "right lobe of liver", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457076 Right Lobe Of Liver
0.719
21.8
38492
1242.4
3092
976.9
4331
167414.5
0.994
title: GSM3633634 WGBS from right lobe of liver (ENCLB061REQ), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "right lobe of liver", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457077 Lower Leg Skin
0.788
29.1
55516
1149.1
3599
924.3
3265
13927.6
0.994
title: GSM3633635 WGBS from lower leg skin (ENCLB672LGT), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "lower leg skin", "sex": "male", "dev_stage": "adult", "age": "37 year", "donor_ID": "ENCDO845WKR", "lab": "Richard Myers, HAIB"}
SRX5457078 Bone Marrow
0.581
28.7
81046
11757.1
3656
1425.6
2428
541249.3
0.994
title: GSM3633636 WGBS from SK-N-SH (ENCLB406PIZ), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "SK-N-SH", "sex": "female", "health_state": "Metastatic neuroblastoma from bone marrow", "dev_stage": "child", "age": "4 year", "donor_ID": "ENCDO000ABD", "lab": "Richard Myers, HAIB"}
SRX5457079 Bone Marrow
0.580
30.0
77405
12317.7
3457
1285.6
2519
521344.3
0.994
title: GSM3633637 WGBS from SK-N-SH (ENCLB721ONH), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "SK-N-SH", "sex": "female", "health_state": "Metastatic neuroblastoma from bone marrow", "dev_stage": "child", "age": "4 year", "donor_ID": "ENCDO000ABD", "lab": "Richard Myers, HAIB"}
SRX5457080 Transverse Colon
0.742
7.8
34504
1413.0
232
874.8
1205
18035.4
0.992
title: GSM3633680 WGBS from transverse colon (ENCLB704GVM), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "transverse colon", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457081 Suprapubic Skin
0.783
24.9
50166
1121.5
2776
944.8
3203
11072.6
0.994
title: GSM3633681 WGBS from suprapubic skin (ENCLB852KRZ), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "suprapubic skin", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457082 Upper Lobe Of Left Lung
0.796
25.6
45023
1144.0
1160
916.5
2842
15494.2
0.993
title: GSM3633682 WGBS from upper lobe of left lung (ENCLB937HGI), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "upper lobe of left lung", "sex": "male", "dev_stage": "adult", "age": "37 year", "donor_ID": "ENCDO845WKR", "lab": "Richard Myers, HAIB"}
SRX5457083 Stomach
0.751
22.6
43669
1144.5
2624
921.6
2740
12555.9
0.994
title: GSM3633683 WGBS from stomach (ENCLB658ATV), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "stomach", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457084 Ovary
0.765
32.6
82752
1123.8
1046
1126.2
3011
13555.2
0.994
title: GSM3633684 WGBS from ovary (ENCLB858YYV), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "ovary", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457085 Heart Left Ventricle
0.756
31.0
50831
1081.3
2866
962.1
3601
19877.3
0.992
title: GSM3633685 WGBS from heart left ventricle (ENCLB439FZB), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "heart left ventricle", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457086 Body Of Pancreas
0.719
23.7
47652
1278.0
938
980.2
3172
27956.1
0.992
title: GSM3633686 WGBS from body of pancreas (ENCLB777VZI), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "body of pancreas", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457087 Hepatocyte
0.796
33.2
55703
1241.6
2358
1029.0
3456
35358.5
0.988
title: GSM3633801 WGBS from hepatocyte (ENCLB409PWJ), Homo sapiens, Bisulfite-Seq; {"age": "5 day", "donor_ID": "ENCDO222AAA", "dev_stage": "embryonic", "sample_type": "in vitro differentiated cells", "cell_type": "hepatocyte", "sex": "female", "health_state": "healthy", "lab": "Richard Myers, HAIB"}
SRX5457088 Hepatocyte
0.798
30.9
54379
1222.4
2151
1054.8
3554
34069.2
0.986
title: GSM3633803 WGBS from hepatocyte (ENCLB757MBA), Homo sapiens, Bisulfite-Seq; {"age": "5 day", "donor_ID": "ENCDO222AAA", "dev_stage": "embryonic", "sample_type": "in vitro differentiated cells", "cell_type": "hepatocyte", "sex": "female", "health_state": "healthy", "lab": "Richard Myers, HAIB"}
SRX5457089 Thyroid Gland
0.820
35.1
60387
1133.7
1112
850.2
3245
19666.0
0.993
title: GSM3633921 WGBS from thyroid gland (ENCLB955VCW), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "thyroid gland", "sex": "male", "dev_stage": "adult", "age": "37 year", "donor_ID": "ENCDO845WKR", "lab": "Richard Myers, HAIB"}
SRX5457090 Cell Line
0.558
31.9
107411
8625.0
542
959.1
3076
392732.6
0.994
title: GSM3633943 WGBS from A549 (ENCLB094KJP), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "A549", "sex": "male", "dev_stage": "adult", "age": "58 year", "donor_ID": "ENCDO000AAZ", "lab": "Richard Myers, HAIB"}
SRX5457091 Cell Line
0.559
33.0
107784
8583.2
578
943.6
3104
391029.4
0.994
title: GSM3633944 WGBS from A549 (ENCLB456FMY), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "A549", "sex": "male", "dev_stage": "adult", "age": "58 year", "donor_ID": "ENCDO000AAZ", "lab": "Richard Myers, HAIB"}
SRX5457092 Esophagus Squamous Epithelium
0.749
16.8
39441
1183.8
1366
945.8
2340
11364.1
0.994
title: GSM3633945 WGBS from esophagus squamous epithelium (ENCLB186SWN), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "esophagus squamous epithelium", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457093 Gastroesophageal Sphincter
0.757
13.2
44133
1230.2
236
952.9
2706
13913.4
0.993
title: GSM3633946 WGBS from gastroesophageal sphincter (ENCLB201VYW), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "gastroesophageal sphincter", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457094 Cell Line
0.602
24.8
109414
8657.8
1136
923.8
3722
324385.1
0.994
title: GSM3633947 WGBS from HeLa-S3 (ENCLB145KPM), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "HeLa-S3", "sex": "female", "health_state": "cervical adenocarcinoma", "dev_stage": "adult", "age": "31 year", "donor_ID": "ENCDO000AAB", "lab": "Richard Myers, HAIB"}
SRX5457095 Cell Line
0.613
36.6
121495
7959.3
1863
929.4
3757
324349.0
0.995
title: GSM3633948 WGBS from HeLa-S3 (ENCLB756LAB), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "HeLa-S3", "sex": "female", "health_state": "cervical adenocarcinoma", "dev_stage": "adult", "age": "31 year", "donor_ID": "ENCDO000AAB", "lab": "Richard Myers, HAIB"}
SRX5457096 Stomach
0.769
24.8
49246
1150.1
2688
972.4
3048
13174.4
0.994
title: GSM3633949 WGBS from stomach (ENCLB479ACS), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "stomach", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457097 Thyroid Gland
0.811
31.5
53827
1101.5
1475
857.9
3119
15899.4
0.993
title: GSM3633950 WGBS from thyroid gland (ENCLB295YNJ), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "thyroid gland", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457098 Fibroblast Of Arm
0.606
31.5
91403
9164.6
774
904.8
3529
320300.2
0.994
title: GSM3633951 WGBS from GM23248 (ENCLB436YZI), Homo sapiens, Bisulfite-Seq; {"age": "53 year", "donor_ID": "ENCDO336AAA", "dev_stage": "adult", "sample_type": "primary cell", "cell_type": "fibroblast of arm", "sex": "male", "lab": "Thomas Gingeras, CSHL"}
SRX5457099 Fibroblast Of Arm
0.605
38.8
92837
9076.3
868
932.5
3487
324001.4
0.994
title: GSM3633952 WGBS from GM23248 (ENCLB777FMV), Homo sapiens, Bisulfite-Seq; {"age": "53 year", "donor_ID": "ENCDO336AAA", "dev_stage": "adult", "sample_type": "primary cell", "cell_type": "fibroblast of arm", "sex": "male", "lab": "Thomas Gingeras, CSHL"}
SRX5457100 Tibial Nerve
0.788
25.1
56447
1120.5
1602
943.8
3288
13311.3
0.994
title: GSM3633953 WGBS from tibial nerve (ENCLB655QZP), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "tibial nerve", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457101 Transverse Colon
0.762
29.0
43717
1154.1
4510
1017.9
2678
10625.1
0.993
title: GSM3633954 WGBS from transverse colon (ENCLB373KCT), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "transverse colon", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457102 Upper Lobe Of Left Lung
0.776
24.9
47497
1102.2
3049
946.6
3070
13392.6
0.993
title: GSM3633955 WGBS from upper lobe of left lung (ENCLB271HNF), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "upper lobe of left lung", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457103 Adrenal Gland
0.770
22.3
42304
1102.6
1535
975.6
2944
13653.1
0.992
title: GSM3633956 WGBS from adrenal gland (ENCLB543VBP), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "adrenal gland", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457104 Spleen
0.771
29.4
44798
1073.8
2175
987.4
2890
11839.4
0.994
title: GSM3633957 WGBS from spleen (ENCLB845KXJ), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "spleen", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457105 Tibial Nerve
0.782
31.1
55830
1122.0
2531
991.9
3036
12705.4
0.994
title: GSM3633958 WGBS from tibial nerve (ENCLB901CGI), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "tibial nerve", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457106 Spleen
0.797
26.6
52121
1038.5
1088
871.0
3361
12664.5
0.994
title: GSM3633974 WGBS from spleen (ENCLB353RJB), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "spleen", "sex": "male", "dev_stage": "adult", "age": "37 year", "donor_ID": "ENCDO845WKR", "lab": "Richard Myers, HAIB"}
SRX5457107 Heart Left Ventricle
0.755
29.6
49146
1089.0
2943
977.6
2780
20932.4
0.993
title: GSM3633975 WGBS from heart left ventricle (ENCLB560LZP), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "heart left ventricle", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457108 Prostate Gland
0.773
27.4
68097
1163.7
2265
899.7
2956
12687.0
0.994
title: GSM3633976 WGBS from prostate gland (ENCLB428IRX), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "prostate gland", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457109 Cell Line
0.450
25.3
78994
13380.7
713
989.8
2383
760468.6
0.993
title: GSM3633977 WGBS from HepG2 (ENCLB890RFU), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "HepG2", "sex": "male", "health_state": "hepatocellular carcinoma", "dev_stage": "child", "age": "15 year", "donor_ID": "ENCDO000AAC", "lab": "Richard Myers, HAIB"}
SRX5457110 Cell Line
0.453
30.5
99139
11287.0
920
1010.5
2379
762812.0
0.994
title: GSM3633978 WGBS from HepG2 (ENCLB443JJF), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "HepG2", "sex": "male", "health_state": "hepatocellular carcinoma", "dev_stage": "child", "age": "15 year", "donor_ID": "ENCDO000AAC", "lab": "Richard Myers, HAIB"}
SRX5457111 Ovary
0.784
34.5
73315
1168.8
1337
1055.2
3126
14219.2
0.994
title: GSM3633985 WGBS from ovary (ENCLB056RXQ), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "ovary", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457112 Testis
0.776
30.0
52837
1330.3
14744
972.2
3660
24879.4
0.993
title: GSM3633986 WGBS from testis (ENCLB095PBB), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "testis", "sex": "male", "dev_stage": "adult", "age": "37 year", "donor_ID": "ENCDO845WKR", "lab": "Richard Myers, HAIB"}
SRX5457113 Gastroesophageal Sphincter
0.756
8.5
40225
1310.0
131
989.3
3009
11923.0
0.993
title: GSM3633989 WGBS from gastroesophageal sphincter (ENCLB515SVA), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "gastroesophageal sphincter", "sex": "female", "dev_stage": "adult", "age": "53 year", "donor_ID": "ENCDO793LXB", "lab": "Richard Myers, HAIB"}
SRX5457114 Esophagus Squamous Epithelium
0.742
18.8
44571
1196.2
1373
872.8
2223
12724.0
0.994
title: GSM3633990 WGBS from esophagus squamous epithelium (ENCLB776RBC), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "esophagus squamous epithelium", "sex": "male", "dev_stage": "adult", "age": "54 year", "donor_ID": "ENCDO451RUA", "lab": "Richard Myers, HAIB"}
SRX5457115 Esophagus Muscularis Mucosa
0.776
22.2
46638
1141.8
1328
1006.3
2895
17096.6
0.993
title: GSM3633991 WGBS from esophagus muscularis mucosa (ENCLB195SCD), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "esophagus muscularis mucosa", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457116 Lower Leg Skin
0.778
26.9
53173
1131.3
4287
983.5
2944
12542.7
0.994
title: GSM3633992 WGBS from lower leg skin (ENCLB460MSR), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "lower leg skin", "sex": "female", "dev_stage": "adult", "age": "51 year", "donor_ID": "ENCDO271OUW", "lab": "Richard Myers, HAIB"}
SRX5457117 Smooth Muscle
0.805
36.1
67680
1216.5
1502
1173.8
3927
34849.8
0.990
title: GSM3633993 WGBS from smooth muscle cell (ENCLB767YYU), Homo sapiens, Bisulfite-Seq; {"age": "5 day", "donor_ID": "ENCDO222AAA", "dev_stage": "embryonic", "sample_type": "in vitro differentiated cells", "cell_type": "smooth muscle cell", "sex": "female", "health_state": "healthy", "lab": "Richard Myers, HAIB"}
SRX5457118 Smooth Muscle
0.809
33.4
66086
1211.7
1567
1162.7
4132
33442.6
0.990
title: GSM3633994 WGBS from smooth muscle cell (ENCLB125PJJ), Homo sapiens, Bisulfite-Seq; {"age": "5 day", "donor_ID": "ENCDO222AAA", "dev_stage": "embryonic", "sample_type": "in vitro differentiated cells", "cell_type": "smooth muscle cell", "sex": "female", "health_state": "healthy", "lab": "Richard Myers, HAIB"}
SRX5457119 Body Of Pancreas
0.722
28.2
50125
1192.0
1985
1003.0
3430
25906.1
0.993
title: GSM3633995 WGBS from body of pancreas (ENCLB417QPU), Homo sapiens, Bisulfite-Seq; {"sample_type": "tissue", "tissue": "body of pancreas", "sex": "male", "dev_stage": "adult", "age": "37 year", "donor_ID": "ENCDO845WKR", "lab": "Richard Myers, HAIB"}
SRX5457120 Cell Line
0.642
36.7
85133
2339.6
3518
1041.1
893
1367756.1
0.994
title: GSM3634061 WGBS from OCI-LY7 (ENCLB588PCW), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "OCI-LY7", "sex": "male", "health_state": "B cell lymphoma", "dev_stage": "adult", "age": "48 year", "donor_ID": "ENCDO351AAA", "lab": "Richard Myers, HAIB"}
SRX5457121 Cell Line
0.640
32.3
79039
2434.0
2781
1021.0
846
1402925.0
0.995
title: GSM3634062 WGBS from OCI-LY7 (ENCLB172JDR), Homo sapiens, Bisulfite-Seq; {"sample_type": "cell line", "cell_line": "OCI-LY7", "sex": "male", "health_state": "B cell lymphoma", "dev_stage": "adult", "age": "48 year", "donor_ID": "ENCDO351AAA", "lab": "Richard Myers, HAIB"}
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
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 .
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