Human methylome studies SRP318399 Track Settings
Study title: DNA methylation profiles of four immune cell types from MS patients and healthy controlsSRA: SRP318399 GEO: GSE173787 Pubmed: 34911760
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
SRX10768293 Blood
0.748
13.2
48971
1158.2
1033
1003.8
2128
10305.3
0.995
title: GSM5278397 MS-1-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768294 Blood
0.804
11.6
54181
1014.7
1059
1022.7
3817
9185.6
0.995
title: GSM5278398 MS-2-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768295 Blood
0.790
13.2
53541
1077.6
1070
979.6
2905
10527.9
0.995
title: GSM5278399 MS-3-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768296 Blood
0.796
12.2
51533
1055.2
1178
973.2
2990
9045.6
0.995
title: GSM5278400 MS-4-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768297 Blood
0.816
12.9
54420
1017.6
1096
1027.5
3801
8586.9
0.995
title: GSM5278401 MS-5-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768298 Blood
0.755
15.6
51852
1058.7
1745
1003.7
2456
9738.5
0.996
title: GSM5278402 MS-6-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768299 Blood
0.773
11.0
49881
1076.8
1482
989.1
2826
8339.0
0.996
title: GSM5278403 MS-7-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768300 Blood
0.782
12.6
51622
1053.9
1325
969.7
2998
9419.8
0.996
title: GSM5278404 MS-8-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768301 Blood
0.791
17.0
56443
1007.7
1916
968.1
2974
10220.6
0.996
title: GSM5278405 MS-9-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768302 Blood
0.758
10.4
49312
1151.9
752
1043.8
2437
9533.5
0.996
title: GSM5278406 MS-10-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768303 Blood
0.779
14.4
53276
1030.6
2109
977.6
2774
10081.5
0.996
title: GSM5278407 MS-11-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768304 Blood
0.775
13.8
51576
1094.8
904
982.0
2648
9660.7
0.996
title: GSM5278408 MS-12-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768305 Blood
0.797
9.1
46324
1165.4
363
948.6
2401
10187.9
0.995
title: GSM5278409 MS-13-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768306 Blood
0.813
11.0
54545
1004.6
733
1044.0
3214
10097.9
0.995
title: GSM5278410 MS-14-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768307 Blood
0.799
12.5
54642
1015.6
1415
972.5
3424
9216.8
0.995
title: GSM5278411 MS-15-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768308 Blood
0.774
11.9
49999
1091.7
1121
1000.4
2736
9511.1
0.995
title: GSM5278412 MS-16-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768309 Blood
0.789
11.4
51609
1058.0
1288
1000.6
2771
10093.2
0.995
title: GSM5278413 MS-17-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768310 Blood
0.812
8.1
50788
1044.0
495
1005.0
1720
15163.4
0.995
title: GSM5278414 MS-18-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768311 Blood
0.789
9.7
50627
1064.1
887
1035.8
2706
9527.6
0.996
title: GSM5278415 MS-19-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768312 Blood
0.804
8.5
51024
1045.0
530
1042.4
1954
15482.7
0.995
title: GSM5278416 MS-20-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768313 Blood
0.793
8.7
48711
1090.9
696
998.5
2955
8994.9
0.996
title: GSM5278417 MS-21-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768314 Blood
0.789
9.7
49648
1077.3
832
1034.0
2804
10124.6
0.995
title: GSM5278418 MS-22-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768315 Blood
0.785
8.3
47467
1112.5
531
1068.3
1667
16705.9
0.996
title: GSM5278419 MS-23-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768317 Blood
0.791
12.9
53678
1010.0
1545
1002.5
3173
8681.4
0.995
title: GSM5278421 MS-25-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768318 Blood
0.824
11.9
56360
995.8
745
1009.1
3545
10059.7
0.995
title: GSM5278422 MS-26-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768319 Blood
0.790
13.2
52020
1025.9
1365
992.6
3049
9003.4
0.994
title: GSM5278423 MS-27-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768320 Blood
0.807
11.9
53551
1019.3
993
1022.3
3184
8868.9
0.995
title: GSM5278424 MS-28-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768321 Blood
0.806
11.8
54082
1013.9
988
992.6
3484
9030.6
0.995
title: GSM5278425 MS-29-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768322 Blood
0.810
11.7
52614
1031.2
757
1020.7
3143
9481.6
0.995
title: GSM5278426 HC-1-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768323 Blood
0.824
11.9
54456
1021.9
677
1035.4
3296
9342.9
0.995
title: GSM5278427 HC-2-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768324 Blood
0.829
14.4
58440
997.3
781
1016.3
3392
10290.4
0.995
title: GSM5278428 HC-3-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768325 Blood
0.804
12.5
53938
1021.9
920
990.3
3263
10779.2
0.995
title: GSM5278429 HC-4-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768326 Blood
0.796
12.5
52568
1051.8
1292
967.2
3017
10562.9
0.995
title: GSM5278430 HC-5-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768327 Blood
0.821
12.2
58971
986.6
1007
1040.6
3465
10518.6
0.995
title: GSM5278431 HC-6-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768328 Blood
0.807
12.5
55535
1010.2
1169
1034.8
3486
9902.5
0.996
title: GSM5278432 HC-7-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768329 Blood
0.794
12.3
53893
998.2
1359
1008.7
3145
8390.1
0.996
title: GSM5278433 HC-8-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768330 Blood
0.789
13.5
53138
1013.1
1541
1007.9
2919
8541.6
0.996
title: GSM5278434 HC-9-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768331 Blood
0.814
13.0
58688
954.3
1038
1016.3
3705
9222.5
0.996
title: GSM5278435 HC-10-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768332 Blood
0.821
17.4
65092
928.0
1383
1023.2
3973
11252.4
0.995
title: GSM5278436 HC-11-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768333 Blood
0.821
17.3
64573
943.8
1378
1017.4
3837
11894.2
0.994
title: GSM5278437 HC-12-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768334 Blood
0.813
7.9
47940
1122.2
273
1041.8
1657
16816.5
0.992
title: GSM5278438 HC-13-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768335 Blood
0.800
7.9
46129
1132.8
438
1045.8
1710
14677.0
0.992
title: GSM5278439 HC-14-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768336 Blood
0.813
7.2
48511
1088.4
208
1020.2
1913
16852.1
0.994
title: GSM5278440 HC-15-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768337 Blood
0.800
9.1
49667
1065.9
759
1000.5
3310
8689.7
0.995
title: GSM5278441 HC-16-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768338 Blood
0.780
8.2
45791
1139.6
583
1013.4
1285
15998.0
0.995
title: GSM5278442 HC-17-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768339 Blood
0.777
8.2
47153
1146.5
498
1010.1
1503
17382.9
0.996
title: GSM5278443 HC-18-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768340 Blood
0.783
13.3
57579
982.5
1745
955.5
3550
10227.5
0.995
title: GSM5278444 HC-19-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768341 Blood
0.820
11.9
56482
988.8
795
1014.0
3634
9925.2
0.995
title: GSM5278445 HC-20-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768343 Blood
0.767
12.1
50474
1122.7
1056
995.3
2425
10350.5
0.994
title: GSM5278447 HC-22-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768344 Blood
0.811
11.8
55055
1026.6
970
1071.8
3256
9792.5
0.994
title: GSM5278448 HC-23-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768345 Blood
0.832
11.3
57134
992.6
644
1107.3
3708
9623.6
0.994
title: GSM5278449 HC-24-CD19BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD19+ B cells"}
SRX10768346 Blood
0.788
13.6
46168
1076.1
723
1004.2
2885
9925.1
0.996
title: GSM5278450 MS-1-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768347 Blood
0.814
13.5
51026
1029.7
911
1012.2
3245
11233.9
0.996
title: GSM5278451 MS-2-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768348 Blood
0.796
12.5
46528
1081.9
770
1026.0
2726
10925.6
0.996
title: GSM5278452 MS-3-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768349 Blood
0.796
12.0
46117
1067.2
787
1060.9
2928
8868.4
0.996
title: GSM5278453 MS-4-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768350 Blood
0.804
13.4
47720
1046.7
788
1059.5
3088
9127.5
0.996
title: GSM5278454 MS-5-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768351 Blood
0.799
13.0
46906
1055.0
728
1060.6
2847
10838.7
0.996
title: GSM5278455 MS-6-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768352 Blood
0.804
9.6
33828
1148.0
261
881.4
1684
13095.7
0.997
title: GSM5278456 MS-7-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768353 Blood
0.813
9.1
41150
1225.3
150
937.5
2377
10652.8
0.996
title: GSM5278457 MS-8-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768354 Blood
0.819
16.1
54432
1013.3
940
992.9
3385
11495.7
0.996
title: GSM5278458 MS-9-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768355 Blood
0.820
15.0
52764
1028.8
819
1016.7
3342
11259.4
0.996
title: GSM5278459 MS-10-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768356 Blood
0.789
9.8
43840
1130.9
635
1026.0
2878
9677.4
0.996
title: GSM5278460 MS-11-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768357 Blood
0.811
11.3
45734
1107.6
466
934.5
2822
10372.9
0.996
title: GSM5278461 MS-12-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768358 Blood
0.782
16.0
47606
1046.8
919
1019.1
2751
10358.7
0.992
title: GSM5278462 MS-13-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768359 Blood
0.810
12.9
47707
1068.2
588
1060.6
3143
9939.0
0.995
title: GSM5278463 MS-14-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768360 Blood
0.826
14.2
54237
1005.8
744
1017.7
3684
10794.5
0.992
title: GSM5278464 MS-15-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768361 Blood
0.799
16.8
53341
999.0
1134
1027.7
3147
10722.4
0.992
title: GSM5278465 MS-16-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768362 Blood
0.773
9.8
41133
1171.6
483
1093.6
2465
9461.1
0.992
title: GSM5278466 MS-17-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768363 Blood
0.801
10.5
44721
1087.6
726
1069.3
3281
8699.8
0.996
title: GSM5278467 HC-1-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768364 Blood
0.798
13.6
47378
1062.6
855
1075.8
3097
8758.7
0.996
title: GSM5278468 HC-2-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768365 Blood
0.797
14.2
48816
1047.2
1056
1010.4
3399
8962.0
0.996
title: GSM5278469 HC-3-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768366 Blood
0.800
11.0
37523
1124.6
448
849.4
2136
13300.1
0.996
title: GSM5278470 HC-4-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768367 Blood
0.796
13.1
47828
1064.9
826
1010.9
2655
11706.5
0.996
title: GSM5278471 HC-5-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768369 Blood
0.824
11.8
49441
1059.3
555
1033.7
3401
11032.1
0.996
title: GSM5278473 HC-7-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768370 Blood
0.802
10.8
45456
1089.6
724
1037.2
2973
8533.6
0.996
title: GSM5278474 HC-8-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768371 Blood
0.740
12.9
40754
1155.1
979
1047.2
1597
9804.4
0.996
title: GSM5278475 HC-9-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768372 Blood
0.815
12.2
42181
1099.3
474
835.2
2285
12554.3
0.996
title: GSM5278476 HC-10-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768373 Blood
0.797
16.7
50772
1017.7
1048
1066.5
3365
10299.6
0.992
title: GSM5278477 HC-11-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768374 Blood
0.800
15.9
51009
1023.6
1007
1048.5
3230
11099.2
0.992
title: GSM5278478 HC-12-CD4BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD4+ T cells"}
SRX10768375 Blood
0.804
12.7
46042
1083.1
628
971.4
3138
10016.6
0.995
title: GSM5278479 MS-1-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768376 Blood
0.804
10.0
45089
1094.7
514
998.8
2981
10292.9
0.995
title: GSM5278480 MS-2-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768377 Blood
0.784
13.1
43537
1121.6
732
1035.7
2754
9849.6
0.996
title: GSM5278481 MS-3-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768378 Blood
0.765
13.0
42762
1108.4
928
1042.0
2104
9258.9
0.996
title: GSM5278482 MS-4-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768379 Blood
0.813
9.7
45542
1085.5
563
1014.1
3456
8677.9
0.995
title: GSM5278483 MS-5-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768380 Blood
0.789
11.6
44245
1074.0
846
1031.2
2401
10715.0
0.995
title: GSM5278484 MS-6-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768381 Blood
0.789
8.2
39865
1175.4
330
1048.0
1448
13615.9
0.996
title: GSM5278485 MS-7-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768382 Blood
0.780
16.4
47143
1048.6
1161
1000.7
2603
10478.5
0.995
title: GSM5278486 MS-8-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768383 Blood
0.786
17.1
49281
1025.0
1361
975.6
2681
10496.2
0.995
title: GSM5278487 MS-9-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768384 Blood
0.821
18.5
54599
986.5
825
854.2
3155
11335.0
0.995
title: GSM5278488 MS-10-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768386 Blood
0.806
8.1
41713
1149.6
281
987.6
1757
16661.1
0.995
title: GSM5278490 MS-12-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768387 Blood
0.758
14.5
43623
1085.3
1189
1020.8
2257
9855.0
0.992
title: GSM5278491 MS-13-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768388 Blood
0.787
14.3
47056
1051.8
1207
1013.1
2831
9650.6
0.992
title: GSM5278492 MS-14-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768389 Blood
0.834
9.1
44025
1127.5
220
953.2
3150
10250.3
0.993
title: GSM5278493 MS-15-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768390 Blood
0.810
14.0
50513
1030.0
919
1028.6
3143
10883.6
0.992
title: GSM5278494 MS-16-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768391 Blood
0.743
15.8
44672
1117.1
923
1095.5
1985
10248.9
0.993
title: GSM5278495 MS-17-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768392 Blood
0.815
13.3
48075
1057.2
848
1034.7
3088
10252.4
0.996
title: GSM5278496 HC-1-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768393 Blood
0.766
13.7
42021
1116.8
1047
1068.0
2178
8949.3
0.996
title: GSM5278497 HC-2-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768394 Blood
0.810
12.2
46668
1070.1
723
1005.0
2918
9955.0
0.996
title: GSM5278498 HC-3-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768395 Blood
0.810
9.2
44612
1114.5
313
972.6
3329
10452.0
0.996
title: GSM5278499 HC-4-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768396 Blood
0.783
11.8
43539
1106.0
914
1011.5
2512
9312.9
0.996
title: GSM5278500 HC-5-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768397 Blood
0.809
9.9
45727
1099.0
442
990.1
3020
11098.0
0.995
title: GSM5278501 HC-6-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768398 Blood
0.832
7.4
46352
1105.6
224
1277.1
2173
17678.9
0.995
title: GSM5278502 HC-7-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768399 Blood
0.776
8.2
38961
1198.6
331
1010.7
1070
14506.5
0.996
title: GSM5278503 HC-8-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768400 Blood
0.705
8.3
35591
1373.2
234
1052.5
1208
11323.6
0.996
title: GSM5278504 HC-9-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768401 Blood
0.823
17.0
57523
980.2
986
1044.7
3416
11872.8
0.995
title: GSM5278505 HC-10-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768402 Blood
0.793
14.6
47600
1038.9
1302
1019.2
3108
10045.3
0.992
title: GSM5278506 HC-11-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768403 Blood
0.815
14.6
51684
1015.9
1079
1026.9
2912
12315.4
0.992
title: GSM5278507 HC-12-CD8BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD8+ T cells"}
SRX10768404 Blood
0.803
11.6
66367
914.4
540
1004.7
3865
10758.0
0.996
title: GSM5278508 MS-1-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768405 Blood
0.803
15.4
74893
866.7
909
1075.3
3836
12050.9
0.996
title: GSM5278509 MS-2-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768407 Blood
0.801
13.0
70208
881.2
811
1047.6
3452
10211.6
0.996
title: GSM5278511 MS-4-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768408 Blood
0.805
11.5
61864
937.9
723
1061.9
3563
9535.6
0.996
title: GSM5278512 MS-5-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768410 Blood
0.802
12.0
59476
967.4
576
1041.2
3482
9593.2
0.996
title: GSM5278514 MS-7-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768412 Blood
0.807
11.2
48527
1012.7
540
926.6
1988
14570.7
0.996
title: GSM5278516 MS-9-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768413 Blood
0.807
13.5
70667
893.1
770
1032.2
3627
11363.7
0.996
title: GSM5278517 MS-10-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768415 Blood
0.797
12.9
59891
962.5
762
981.5
3081
11185.4
0.996
title: GSM5278519 MS-12-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Multiple sclerosis", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768416 Blood
0.799
11.7
65679
908.8
894
1070.8
3546
10088.0
0.996
title: GSM5278520 HC-1-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768417 Blood
0.804
13.6
71683
874.4
882
1083.8
3972
9349.9
0.996
title: GSM5278521 HC-2-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768418 Blood
0.800
14.1
73299
866.7
861
1027.1
3709
10518.3
0.996
title: GSM5278522 HC-3-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768419 Blood
0.800
11.6
64691
924.9
655
1032.3
3714
11774.1
0.996
title: GSM5278523 HC-4-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768420 Blood
0.791
16.9
77303
849.1
1084
1042.1
3569
12874.7
0.996
title: GSM5278524 HC-5-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768421 Blood
0.805
11.6
64836
922.5
726
1064.1
3373
10914.5
0.996
title: GSM5278525 HC-6-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768422 Blood
0.804
11.8
63094
933.1
586
1118.9
3433
11139.9
0.996
title: GSM5278526 HC-7-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768423 Blood
0.799
11.0
62045
945.9
682
1080.3
3217
9383.6
0.996
title: GSM5278527 HC-8-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768424 Blood
0.790
14.7
64884
921.3
1082
1038.3
3393
8771.8
0.996
title: GSM5278528 HC-9-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
SRX10768425 Blood
0.797
10.9
55937
986.8
884
990.6
3270
9651.6
0.996
title: GSM5278529 HC-10-CD14BS-Seq, Homo sapiens, Bisulfite-Seq; {"source_name": "peripheral blood", "disease": "Healthy control", "tissue": "peripheral blood", "cell_type": "CD14+ monocytes"}
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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