Human methylome studies SRP126677 Track Settings
Study title: Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS]SRA: SRP126677 GEO: GSE107729 Pubmed: 31288836
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
SRX3468746 Brain
0.805
17.7
63875
1406.8
11108
994.9
5366
21670.0
0.950
title: GSM2877162 1535_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1535", "age": "52", "disease": "Control", "sex": "male"}
SRX3468747 Brain
0.744
14.5
53131
1268.8
10236
2695.9
4581
18612.8
0.953
title: GSM2877163 1516_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1516", "age": "47", "disease": "Schizo", "sex": "male"}
SRX3468748 Brain
0.798
13.4
54021
1283.7
6828
949.9
4994
20150.5
0.952
title: GSM2877164 1509_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1509", "age": "52", "disease": "Schizo", "sex": "male"}
SRX3468749 Brain
0.797
15.6
55355
1258.7
7204
3421.6
4951
20912.2
0.960
title: GSM2877165 1519_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1519", "age": "54", "disease": "Schizo", "sex": "male"}
SRX3468750 Brain
0.812
13.6
56580
1324.9
6972
945.8
5420
20776.5
0.950
title: GSM2877166 1533_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1533", "age": "54", "disease": "Control", "sex": "male"}
SRX3468751 Brain
0.780
17.0
53202
1288.2
12205
1011.3
4377
20423.0
0.962
title: GSM2877167 1537_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1537", "age": "46", "disease": "Control", "sex": "male"}
SRX3468752 Brain
0.824
29.0
72408
1628.3
9875
940.0
6521
22353.2
0.943
title: GSM2877168 1517_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1517", "age": "77", "disease": "Schizo", "sex": "male"}
SRX3468753 Brain
0.785
34.0
68840
1489.1
7388
937.7
5107
20145.1
0.943
title: GSM2877169 1531_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1531", "age": "60", "disease": "Control", "sex": "male"}
SRX3468754 Brain
0.763
30.8
71138
1515.7
7249
969.9
5670
19590.9
0.949
title: GSM2877170 1534_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1534", "age": "75", "disease": "Control", "sex": "male"}
SRX3468755 Brain
0.810
30.1
65144
1653.0
14231
1025.6
4932
52028.2
0.953
title: GSM2877171 1512_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1512", "age": "43", "disease": "Schizo", "sex": "female"}
SRX3468756 Brain
0.785
26.3
77970
1332.0
1609
1025.0
4280
43131.0
0.989
title: GSM2877172 1512_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1512", "age": "43", "disease": "Schizo", "sex": "female"}
SRX3468757 Brain
0.779
28.7
79921
1308.4
1338
1042.5
4417
43396.4
0.989
title: GSM2877173 1523_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1523", "age": "42", "disease": "Schizo", "sex": "female"}
SRX3468758 Brain
0.797
25.5
60876
1454.0
14108
1017.3
4883
22259.2
0.951
title: GSM2877174 1524_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1524", "age": "40", "disease": "Control", "sex": "male"}
SRX3468759 Brain
0.816
32.5
71976
1693.5
13194
992.6
5138
48462.7
0.934
title: GSM2877175 4336_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "4336", "age": "85", "disease": "Schizo", "sex": "female"}
SRX3468760 Brain
0.830
34.5
60168
1802.8
20889
1090.1
4706
29311.6
0.904
title: GSM2877176 3545_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "3545", "age": "80", "disease": "Control", "sex": "male"}
SRX3468761 Brain
0.799
39.0
77506
1478.2
1508
901.5
4079
30692.7
0.977
title: GSM2877177 3545_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "3545", "age": "80", "disease": "Control", "sex": "male"}
SRX3468762 Brain
0.828
38.1
76011
1736.7
13085
978.0
6481
24589.6
0.927
title: GSM2877178 3586_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "3586", "age": "76", "disease": "Control", "sex": "male"}
SRX3468763 Brain
0.810
33.0
74245
1860.7
13141
1012.1
4503
63060.4
0.952
title: GSM2877179 1505_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1505", "age": "46", "disease": "Schizo", "sex": "female"}
SRX3468764 Brain
0.800
37.0
69350
1463.5
5679
972.1
4251
46550.6
0.986
title: GSM2877180 1505_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1505", "age": "46", "disease": "Schizo", "sex": "female"}
SRX3468765 Brain
0.807
28.9
68697
1613.3
13089
992.3
4714
55203.6
0.947
title: GSM2877181 1523_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1523", "age": "42", "disease": "Schizo", "sex": "female"}
SRX3468766 Brain
0.793
27.9
80805
1287.1
1098
1079.8
4361
43451.7
0.987
title: GSM2877182 4336_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "4336", "age": "85", "disease": "Schizo", "sex": "female"}
SRX3468767 Brain
0.785
23.1
76574
1229.4
2605
912.4
4402
22789.5
0.990
title: GSM2877183 1524_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1524", "age": "40", "disease": "Control", "sex": "male"}
SRX3468768 Brain
0.798
34.5
84275
1357.9
820
893.9
4319
28170.0
0.987
title: GSM2877184 3586_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "3586", "age": "76", "disease": "Control", "sex": "male"}
SRX3468769 Brain
0.815
30.1
74587
1717.8
11127
977.4
4897
55548.9
0.943
title: GSM2877185 4361_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "4361", "age": "77", "disease": "Schizo", "sex": "female"}
SRX3468774 Brain
0.808
39.1
78284
1414.6
1024
891.2
3921
31596.7
0.983
title: GSM2877190 1507_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1507", "age": "32", "disease": "Schizo", "sex": "male"}
SRX3468775 Brain
0.808
25.1
69766
1626.8
12560
988.6
4258
61643.0
0.954
title: GSM2877191 1508_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1508", "age": "73", "disease": "Schizo", "sex": "female"}
SRX3468776 Brain
0.820
25.3
66333
1625.4
14229
1018.9
5210
25462.9
0.950
title: GSM2877192 1510_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1510", "age": "33", "disease": "Schizo", "sex": "male"}
SRX3468777 Brain
0.821
28.5
73799
1692.3
13301
996.8
6047
27861.2
0.949
title: GSM2877193 1511_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1511", "age": "26", "disease": "Schizo", "sex": "male"}
SRX3468778 Brain
0.821
33.0
67034
1735.3
14955
1033.4
4622
54167.3
0.952
title: GSM2877194 1513_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1513", "age": "73", "disease": "Schizo", "sex": "female"}
SRX3468779 Brain
0.820
36.5
67174
1732.9
16511
1042.2
5726
24724.0
0.953
title: GSM2877195 1514_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1514", "age": "40", "disease": "Schizo", "sex": "male"}
SRX3468780 Brain
0.821
34.9
69022
1798.0
13706
1007.5
3998
65705.7
0.953
title: GSM2877196 1515_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1515", "age": "50", "disease": "Schizo", "sex": "female"}
SRX3468781 Brain
0.817
33.5
71848
1795.6
12863
994.1
4740
57699.6
0.947
title: GSM2877197 1518_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1518", "age": "52", "disease": "Schizo", "sex": "female"}
SRX3468782 Brain
0.814
33.4
69508
1808.8
14712
1020.9
4460
59770.0
0.950
title: GSM2877198 1525_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1525", "age": "65", "disease": "Control", "sex": "female"}
SRX3468783 Brain
0.803
25.4
79251
1300.3
663
1000.4
3773
30012.2
0.991
title: GSM2877199 1511_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1511", "age": "26", "disease": "Schizo", "sex": "male"}
SRX3468784 Brain
0.808
31.2
72010
1770.5
13536
997.4
5759
28797.8
0.950
title: GSM2877200 1527_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1527", "age": "36", "disease": "Control", "sex": "male"}
SRX3468785 Brain
0.805
35.4
73770
1783.2
14035
1003.8
4600
57692.0
0.936
title: GSM2877201 1532_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1532", "age": "68", "disease": "Control", "sex": "female"}
SRX3468786 Brain
0.808
30.4
70695
1646.8
13774
996.2
5794
24990.3
0.948
title: GSM2877202 1536_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1536", "age": "41", "disease": "Control", "sex": "male"}
SRX3468787 Brain
0.809
35.1
73704
1700.6
12695
988.7
5051
50227.1
0.944
title: GSM2877203 1538_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1538", "age": "55", "disease": "Control", "sex": "female"}
SRX3468788 Brain
0.808
32.7
69674
1764.5
14073
1006.1
4288
64452.6
0.950
title: GSM2877204 1539_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1539", "age": "53", "disease": "Control", "sex": "female"}
SRX3468789 Brain
0.810
35.0
72658
1728.4
14789
1017.4
5368
48134.7
0.931
title: GSM2877205 1541_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1541", "age": "49", "disease": "Control", "sex": "female"}
SRX3468790 Brain
0.799
40.6
65274
1858.3
19158
1076.3
5240
26513.2
0.951
title: GSM2877206 3602_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "3602", "age": "66", "disease": "Control", "sex": "male"}
SRX3468791 Brain
0.819
37.4
68501
1694.3
17095
1014.6
5147
24784.8
0.951
title: GSM2877207 3611_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "3611", "age": "64", "disease": "Control", "sex": "male"}
SRX3468792 Brain
0.818
34.9
58519
1654.9
15173
1019.3
4166
55952.5
0.944
title: GSM2877208 AN03398_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN03398", "age": "75", "disease": "Control", "sex": "female"}
SRX3468793 Brain
0.805
33.3
78125
1763.6
15157
1018.0
5279
48722.4
0.922
title: GSM2877209 AN15240_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN15240", "age": "36", "disease": "Control", "sex": "female"}
SRX3468794 Brain
0.834
46.6
79170
2210.3
31195
1197.6
5469
31179.5
0.924
title: GSM2877210 AN16799_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN16799", "age": "43", "disease": "Control", "sex": "male"}
SRX3468796 Brain
0.798
37.4
78557
1385.8
831
896.6
4032
28765.3
0.991
title: GSM2877212 4615_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "4615", "age": "49", "disease": "Control", "sex": "male"}
SRX3468797 Brain
0.825
32.6
69534
1624.1
13539
982.9
6308
21486.7
0.947
title: GSM2877213 AN05483_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN05483", "age": "66", "disease": "Control", "sex": "male"}
SRX3468798 Brain
0.797
33.5
84063
1253.0
720
939.6
4265
24780.6
0.991
title: GSM2877214 AN05483_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "AN05483", "age": "66", "disease": "Control", "sex": "male"}
SRX3468799 Brain
0.810
35.6
72628
1763.5
15049
1006.0
6310
24577.0
0.945
title: GSM2877215 AN10090_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN10090", "age": "52", "disease": "Control", "sex": "male"}
SRX3468800 Brain
0.794
39.1
78730
1433.8
1429
1086.4
4557
41342.1
0.991
title: GSM2877216 1532_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1532", "age": "68", "disease": "Control", "sex": "female"}
SRX3468801 Brain
0.790
37.2
78983
1448.4
1634
1075.2
4367
47139.2
0.991
title: GSM2877217 1539_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1539", "age": "53", "disease": "Control", "sex": "female"}
SRX3468802 Brain
0.791
28.3
87030
1238.4
511
927.3
3193
33580.7
0.990
title: GSM2877218 AN10090_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "AN10090", "age": "52", "disease": "Control", "sex": "male"}
SRX3468803 Brain
0.787
43.2
80969
1479.2
1106
900.9
3953
30734.7
0.992
title: GSM2877219 1527_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1527", "age": "36", "disease": "Control", "sex": "male"}
SRX3468804 Brain
0.802
25.7
83674
1279.0
483
946.1
4011
30137.9
0.981
title: GSM2877220 1536_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1536", "age": "41", "disease": "Control", "sex": "male"}
SRX3468805 Brain
0.789
38.2
76258
1389.0
2857
1003.0
5132
33057.0
0.990
title: GSM2877221 1538_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1538", "age": "55", "disease": "Control", "sex": "female"}
SRX3468807 Brain
0.839
25.8
63567
1612.6
10663
961.8
5546
25719.5
0.939
title: GSM2877223 4395_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "4395", "age": "56", "disease": "Schizo", "sex": "male"}
SRX3468808 Brain
0.798
33.3
81835
1332.0
709
923.7
4329
28335.4
0.989
title: GSM2877224 4395_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "4395", "age": "56", "disease": "Schizo", "sex": "male"}
SRX3468809 Brain
0.801
22.4
70541
1571.7
13915
1006.0
5339
25185.1
0.916
title: GSM2877225 4504_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "4504", "age": "55", "disease": "Schizo", "sex": "male"}
SRX3468810 Brain
0.784
27.9
78557
1365.9
1521
1101.8
4197
46844.7
0.991
title: GSM2877226 AN17799_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "AN17799", "age": "56", "disease": "Schizo", "sex": "female"}
SRX3468811 Brain
0.815
40.8
71070
1840.7
14465
997.3
5743
28026.4
0.947
title: GSM2877227 4448_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "4448", "age": "46", "disease": "Schizo", "sex": "male"}
SRX3468812 Brain
0.821
34.6
67713
1636.0
13236
987.1
5801
23784.4
0.948
title: GSM2877228 3590_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "3590", "age": "75", "disease": "Control", "sex": "male"}
SRX3468813 Brain
0.807
30.5
78860
1465.2
10871
1081.2
3866
32079.1
0.930
title: GSM2877229 3590_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "3590", "age": "75", "disease": "Control", "sex": "male"}
SRX3468814 Brain
0.800
42.0
73579
1469.5
4547
941.4
4137
29746.0
0.980
title: GSM2877230 1520_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1520", "age": "38", "disease": "Schizo", "sex": "male"}
SRX3468815 Brain
0.795
37.5
83283
1495.9
1435
1036.2
3683
57648.9
0.976
title: GSM2877231 1525_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1525", "age": "65", "disease": "Control", "sex": "female"}
SRX3468816 Brain
0.809
32.1
72650
1830.2
14217
1016.2
4592
59850.0
0.950
title: GSM2877232 AN17799_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN17799", "age": "56", "disease": "Schizo", "sex": "female"}
SRX3468817 Brain
0.800
37.7
77852
1483.9
1976
885.0
3975
31473.9
0.970
title: GSM2877233 4448_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "4448", "age": "46", "disease": "Schizo", "sex": "male"}
SRX3468818 Brain
0.792
37.3
76624
1341.3
789
936.5
3904
27876.4
0.990
title: GSM2877234 4504_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "4504", "age": "55", "disease": "Schizo", "sex": "male"}
SRX3468819 Brain
0.801
42.7
80250
1437.9
1068
903.0
4229
27819.7
0.990
title: GSM2877235 3602_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "3602", "age": "66", "disease": "Control", "sex": "male"}
SRX3468820 Brain
0.813
43.0
82240
1426.0
5222
971.3
4043
29982.2
0.942
title: GSM2877236 3611_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "3611", "age": "64", "disease": "Control", "sex": "male"}
SRX3468821 Brain
0.791
46.0
78546
1532.0
1054
916.0
3822
31969.0
0.989
title: GSM2877237 4804_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "4804", "age": "61", "disease": "Schizo", "sex": "male"}
SRX3468822 Brain
0.793
43.9
80480
1495.5
1635
1060.0
4927
40842.7
0.991
title: GSM2877238 AN03398_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "AN03398", "age": "75", "disease": "Control", "sex": "female"}
SRX3468823 Brain
0.785
44.2
79347
1569.2
1706
1071.6
4241
47315.1
0.989
title: GSM2877239 AN15240_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "AN15240", "age": "36", "disease": "Control", "sex": "female"}
SRX3468824 Brain
0.783
48.1
82933
1586.4
3501
873.7
3998
29610.8
0.989
title: GSM2877240 AN16799_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "AN16799", "age": "43", "disease": "Control", "sex": "male"}
SRX3468825 Brain
0.799
43.7
82802
1785.7
9136
951.3
6588
25334.9
0.947
title: GSM2877241 4804_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "4804", "age": "61", "disease": "Schizo", "sex": "male"}
SRX3468826 Brain
0.795
43.8
81717
1358.9
809
940.3
3776
28084.1
0.986
title: GSM2877242 Miami0001_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "Miami0001", "age": "25", "disease": "Control", "sex": "male"}
SRX3468827 Brain
0.819
38.5
64824
1723.4
14557
1009.1
5491
26953.8
0.955
title: GSM2877243 AN09634_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN09634", "age": "26", "disease": "Schizo", "sex": "male"}
SRX3468828 Brain
0.811
39.3
71366
1783.3
13228
1001.8
5181
48627.2
0.950
title: GSM2877244 4730_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "4730", "age": "32", "disease": "Schizo", "sex": "female"}
SRX3468829 Brain
0.798
29.6
57182
1481.3
11424
961.3
4030
26465.1
0.965
title: GSM2877245 AN18099_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "AN18099", "age": "66", "disease": "Schizo", "sex": "male"}
SRX3468830 Brain
0.813
29.6
71166
1511.9
8888
941.2
6174
21246.8
0.948
title: GSM2877246 1521_WGBS_NeuN, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "NeuN", "subject_id": "1521", "age": "60", "disease": "Schizo", "sex": "male"}
SRX3468832 Brain
0.795
35.4
79484
1435.7
1716
1052.5
4720
42436.5
0.990
title: GSM2877248 1513_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1513", "age": "73", "disease": "Schizo", "sex": "female"}
SRX3468833 Brain
0.787
38.7
77852
1362.3
1456
920.4
4204
24851.5
0.988
title: GSM2877249 1514_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1514", "age": "40", "disease": "Schizo", "sex": "male"}
SRX3468834 Brain
0.794
34.6
80180
1414.0
1072
1098.9
4015
52168.5
0.989
title: GSM2877250 1515_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1515", "age": "50", "disease": "Schizo", "sex": "female"}
SRX3468835 Brain
0.780
35.6
81198
1450.0
1382
1111.4
3929
53264.2
0.989
title: GSM2877251 1518_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "1518", "age": "52", "disease": "Schizo", "sex": "female"}
SRX3468836 Brain
0.806
34.2
78103
1391.6
527
1022.0
3925
30700.8
0.989
title: GSM2877252 AN18099_WGBS_Olig2, Homo sapiens, Bisulfite-Seq; {"source_name": "Brain BA46", "tissue": "brain", "brain_region": "Brodmann Area 46 (BA46)", "cell_type": "Olig2", "subject_id": "AN18099", "age": "66", "disease": "Schizo", "sex": "male"}
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 .
Top⇑ Top⇑