Mouse methylome studies SRP456835 Track Settings
Study title: DNMT3A AddbackSRA: SRP456835 GEO: not foundPubmed: not found
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
SRX21474919 Bone Marrow
0.753
13.5
49538
1025.1
808
950.0
2917
7450.9
0.987
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "1"}
SRX21474920 Bone Marrow
0.731
15.1
47328
988.6
439
949.0
1368
10940.7
0.979
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "2", "sample_number": "2"}
SRX21474921 Bone Marrow
0.706
15.3
61605
1026.4
679
1010.7
2227
14142.0
0.978
title: 3a KO; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "2", "sample_number": "11"}
SRX21474922 Bone Marrow
0.774
8.0
43884
1176.3
172
1143.5
909
14528.2
0.977
title: R878H het addback EV; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "1", "sample_number": "44"}
SRX21474923 Bone Marrow
0.783
7.4
37714
1188.7
144
1273.4
771
14338.8
0.977
title: R878H het addback 3A; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "1", "sample_number": "45"}
SRX21474924 Bone Marrow
0.788
6.9
35233
1270.5
123
1162.0
709
14883.6
0.976
title: R878H het addback 3l; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "1", "sample_number": "46"}
SRX21474925 Bone Marrow
0.773
10.3
48425
1094.0
205
1093.3
1364
11071.0
0.979
title: R878H het addback EV; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "2", "sample_number": "47"}
SRX21474926 Bone Marrow
0.785
11.9
43539
1098.8
239
1080.3
1345
10806.6
0.977
title: R878H het addback 3A; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "2", "sample_number": "48"}
SRX21474927 Bone Marrow
0.787
6.8
35631
1276.5
113
1232.7
958
13511.6
0.977
title: R878H het addback 3l; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "2", "sample_number": "49"}
SRX21474928 Bone Marrow
0.766
14.2
57275
1026.2
639
1080.6
3210
7283.1
0.981
title: R878H het addback EV; {"strain": "C57BL/6J", "age": "9w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "3", "sample_number": "50"}
SRX21474929 Bone Marrow
0.767
8.1
48077
1121.1
275
941.3
946
18113.2
0.983
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "6", "sample_number": "6"}
SRX21474930 Bone Marrow
0.784
7.5
37544
1162.8
244
1123.2
764
14240.5
0.979
title: R878H het addback 3A; {"strain": "C57BL/6J", "age": "9w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "3", "sample_number": "51"}
SRX21474931 Bone Marrow
0.778
9.8
42526
1153.2
343
1111.9
1372
10572.8
0.981
title: R878H het addback 3l; {"strain": "C57BL/6J", "age": "9w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "3", "sample_number": "52"}
SRX21474932 Bone Marrow
0.769
6.8
45688
1246.0
191
1071.9
1140
17971.4
0.977
title: in vivo R878H het addback EV; {"strain": "C57BL/6J", "age": "3m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "1", "sample_number": "53"}
SRX21474933 Bone Marrow
0.772
5.8
37883
1330.3
118
1207.9
911
15701.2
0.976
title: in vivo R878H het addback 3A; {"strain": "C57BL/6J", "age": "3m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "1", "sample_number": "54"}
SRX21474934 Bone Marrow
0.792
6.9
40500
1289.3
158
944.8
717
19063.6
0.979
title: in vivo R878H het addback 3L; {"strain": "C57BL/6J", "age": "3m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "1", "sample_number": "55"}
SRX21474935 Bone Marrow
0.799
8.0
39430
1129.5
195
992.8
808
15992.1
0.982
title: in vivo R878H het addback 3A; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "2", "sample_number": "56"}
SRX21474936 Bone Marrow
0.803
9.3
40646
1094.6
228
989.3
1170
11464.5
0.981
title: in vivo R878H het addback 3A; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "3", "sample_number": "57"}
SRX21474937 Bone Marrow
0.779
8.2
44172
1132.3
204
1029.3
1134
12029.5
0.983
title: in vivo R878H het addback 3A; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "4", "sample_number": "58"}
SRX21474938 Bone Marrow
0.692
17.2
60669
1030.4
688
1083.3
2183
14103.2
0.984
title: 3a KO; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "3", "sample_number": "12"}
SRX21474939 Bone Marrow
0.711
16.1
66718
1026.8
666
1074.2
2544
15545.4
0.984
title: 3a KO; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "4", "sample_number": "13"}
SRX21474940 Bone Marrow
0.699
15.3
54192
998.3
363
1014.3
1601
12399.0
0.984
title: 3b KO; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "14"}
SRX21474941 Bone Marrow
0.722
13.1
53978
1019.4
350
1072.4
1506
12712.0
0.980
title: 3b KO; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "2", "sample_number": "15"}
SRX21474942 Bone Marrow
0.708
13.2
56548
1039.0
374
989.8
1873
12498.0
0.982
title: 3b KO; {"strain": "C57BL/6J", "age": "15w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "3", "sample_number": "16"}
SRX21474943 Bone Marrow
0.620
7.9
48873
1454.3
147
1041.2
1413
21926.9
0.982
title: DKO; {"strain": "C57BL/6J", "age": "15w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "17"}
SRX21474944 Bone Marrow
0.683
7.0
53662
1410.9
117
1118.4
1887
24849.2
0.982
title: DKO; {"strain": "C57BL/6J", "age": "15w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "2", "sample_number": "18"}
SRX21474945 Bone Marrow
0.682
10.8
61849
1165.2
287
1007.6
2522
16115.8
0.983
title: DKO; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "3", "sample_number": "19"}
SRX21474946 Bone Marrow
0.686
7.0
40318
1318.9
163
1034.6
912
15211.9
0.983
title: R878H het; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "1", "sample_number": "20"}
SRX21474947 Bone Marrow
0.701
9.3
41982
1111.7
449
988.8
1088
11014.2
0.984
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "3", "sample_number": "3"}
SRX21474948 Bone Marrow
0.695
8.4
44834
1200.9
282
1021.4
1436
11944.2
0.983
title: R878H het; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "2", "sample_number": "21"}
SRX21474949 Bone Marrow
0.699
7.5
44156
1275.1
201
1021.2
971
16217.2
0.983
title: R878H het; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "3", "sample_number": "22"}
SRX21474950 Bone Marrow
0.753
9.1
55140
1111.4
277
953.2
1881
13319.8
0.982
title: R878H het; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "4", "sample_number": "23"}
SRX21474951 Bone Marrow
0.746
9.5
54657
1114.0
342
939.7
1769
13279.5
0.980
title: R878H het; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "5", "sample_number": "24"}
SRX21474952 Bone Marrow
0.684
7.8
45227
1238.9
278
1025.9
1069
16682.6
0.983
title: R878H het; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "6", "sample_number": "25"}
SRX21474953 Bone Marrow
0.801
9.9
40456
1127.9
296
1036.9
1323
11505.1
0.981
title: 3a KO addback; {"strain": "C57BL/6J", "age": "10w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "26"}
SRX21474954 Bone Marrow
0.793
5.5
36346
1408.6
74
1095.3
862
18015.0
0.980
title: 3a KO addback; {"strain": "C57BL/6J", "age": "10w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "27"}
SRX21474955 Bone Marrow
0.772
8.2
53624
1129.9
198
3343.8
2077
12526.2
0.981
title: 3a KO addback; {"strain": "C57BL/6J", "age": "10w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "28"}
SRX21474956 Bone Marrow
0.775
6.4
47652
1215.9
123
4601.0
1348
17760.5
0.982
title: 3a KO addback; {"strain": "C57BL/6J", "age": "10w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "29"}
SRX21474957 Bone Marrow
0.813
8.0
37647
1087.9
460
1013.6
1248
12153.4
0.981
title: WT addback in vivo 3A; {"strain": "C57BL/6J", "age": "5m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "73"}
SRX21474958 Bone Marrow
0.754
7.3
34754
1265.3
232
997.8
741
15631.2
0.979
title: WT addback in vivo 3L; {"strain": "C57BL/6J", "age": "4m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "74"}
SRX21474959 Bone Marrow
0.786
9.6
37595
1197.7
478
921.9
1306
11964.1
0.980
title: WT addback in vivo 3L; {"strain": "C57BL/6J", "age": "5m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "75"}
SRX21474965 Bone Marrow
0.766
11.1
49537
1052.3
414
924.8
1684
11290.4
0.983
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "9", "sample_number": "9"}
SRX21474966 Bone Marrow
0.713
14.4
64102
1062.2
469
897.5
3787
10318.0
0.987
title: 3a KO; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "10"}
SRX21474967 Bone Marrow
0.773
6.1
47831
1232.3
92
1123.5
1324
18142.6
0.983
title: 3a KO addback; {"strain": "C57BL/6J", "age": "10w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "30"}
SRX21474968 Bone Marrow
0.766
7.8
43806
1141.7
243
1000.7
852
16735.8
0.981
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "4", "sample_number": "4"}
SRX21474969 Bone Marrow
0.808
7.6
35212
1207.1
155
1177.3
1301
10746.2
0.982
title: 3b KO addback; {"strain": "C57BL/6J", "age": "12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "31"}
SRX21474970 Bone Marrow
0.794
7.4
38906
1147.5
178
1163.2
1041
13933.9
0.983
title: 3b KO addback; {"strain": "C57BL/6J", "age": "12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "32"}
SRX21474971 Bone Marrow
0.804
7.6
36604
1141.3
160
1147.7
1286
10602.4
0.982
title: 3b KO addback; {"strain": "C57BL/6J", "age": "12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "33"}
SRX21474972 Bone Marrow
0.790
7.0
43897
1137.3
133
1160.3
1140
15750.9
0.982
title: 3b KO addback; {"strain": "C57BL/6J", "age": "12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "34"}
SRX21474973 Bone Marrow
0.786
5.9
39480
1190.8
113
1121.9
789
15981.1
0.983
title: 3b KO addback; {"strain": "C57BL/6J", "age": "12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "35"}
SRX21474974 Bone Marrow
0.816
6.0
34944
1280.3
36
1114.3
1091
16023.7
0.979
title: DKO addback; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "36"}
SRX21474975 Bone Marrow
0.787
10.1
45417
1289.7
188
1084.9
1978
13650.8
0.981
title: DKO addback; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "37"}
SRX21474976 Bone Marrow
0.759
8.7
58957
1129.2
225
1045.6
2188
14920.4
0.983
title: DKO addback; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "38"}
SRX21474977 Bone Marrow
0.774
7.8
54265
1193.3
146
4021.8
2147
14191.6
0.982
title: DKO addback; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "39"}
SRX21474978 Bone Marrow
0.789
7.4
49580
1338.0
94
990.3
1846
14446.0
0.981
title: DKO addback; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3bfl//flxDnmt3bfl//flx VAVcre", "replicate": "1", "sample_number": "40"}
SRX21474979 Bone Marrow
0.751
13.4
48725
1026.1
533
887.8
1521
11483.1
0.987
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "5", "sample_number": "5"}
SRX21474980 Bone Marrow
0.787
11.7
45676
1102.7
253
1044.5
1505
12036.7
0.984
title: 3a KO addback 3A; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "41"}
SRX21474981 Bone Marrow
0.771
10.2
55747
1119.8
256
1015.4
1737
14081.8
0.984
title: 3a KO addback 3L; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "42"}
SRX21474982 Bone Marrow
0.768
10.9
58324
1078.9
282
979.6
2030
13206.2
0.984
title: 3a KO addback EV; {"strain": "C57BL/6J", "age": "6w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3afl//flx VAVcre", "replicate": "1", "sample_number": "43"}
SRX21474983 Bone Marrow
0.791
7.9
39879
1251.7
177
985.3
1293
12133.8
0.983
title: in vivo R878H het addback 3L; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "2", "sample_number": "59"}
SRX21474984 Bone Marrow
0.772
6.5
42305
1264.9
167
1022.7
702
19701.9
0.982
title: in vivo R878H het addback EV; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "2", "sample_number": "60"}
SRX21474985 Bone Marrow
0.743
12.9
46670
1026.0
364
1000.8
1027
15202.3
0.979
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "7", "sample_number": "7"}
SRX21474986 Bone Marrow
0.785
7.2
48166
1187.9
188
1017.6
1066
18486.0
0.982
title: in vivo R878H het addback EV; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "3", "sample_number": "61"}
SRX21474987 Bone Marrow
0.772
7.9
45530
1188.3
221
983.8
1593
11771.8
0.983
title: in vivo R878H het addback EV; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "4", "sample_number": "62"}
SRX21474988 Bone Marrow
0.799
7.6
39469
1231.2
167
910.9
1028
16032.5
0.983
title: in vivo R878H het addback 3L; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "3", "sample_number": "63"}
SRX21474989 Bone Marrow
0.779
8.5
42195
1181.2
309
929.8
1426
11391.0
0.983
title: in vivo R878H het addback 3L; {"strain": "C57BL/6J", "age": "6m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3aR878H/+", "replicate": "4", "sample_number": "64"}
SRX21474990 Bone Marrow
0.789
10.2
42806
1066.9
391
1091.0
1259
9892.6
0.980
title: WT addback ex vivo EV; {"strain": "C57BL/6J", "age": "9w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "65"}
SRX21474991 Bone Marrow
0.789
7.8
36219
1142.8
201
1056.2
797
12832.1
0.982
title: WT addback ex vivo EV; {"strain": "C57BL/6J", "age": "12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "2", "sample_number": "66"}
SRX21474992 Bone Marrow
0.794
5.9
35955
1232.6
74
1089.8
900
14299.5
0.982
title: WT addback ex vivo EV; {"strain": "C57BL/6J", "age": "10w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "3", "sample_number": "67"}
SRX21474993 Bone Marrow
0.810
10.8
40494
1096.3
347
1027.9
1256
11073.6
0.981
title: WT addback ex vivo EV; {"strain": "C57BL/6J", "age": "7w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "4", "sample_number": "68"}
SRX21474994 Bone Marrow
0.797
8.8
39253
1061.1
477
1091.3
1076
10437.2
0.983
title: WT addback ex vivo EV; {"strain": "C57BL/6J", "age": "16w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "female", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "5", "sample_number": "69"}
SRX21474995 Bone Marrow
0.787
9.5
43740
1123.8
448
977.1
1581
11428.6
0.981
title: WT addback in vivo EV; {"strain": "C57BL/6J", "age": "4m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "70"}
SRX21474996 Bone Marrow
0.717
17.1
46398
986.4
417
1001.6
1156
11799.1
0.984
title: WT; {"strain": "C57BL/6J", "age": "6w-12w", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "8", "sample_number": "8"}
SRX21474997 Bone Marrow
0.696
9.1
39967
1176.5
428
1901.9
976
11601.8
0.982
title: WT addback in vivo EV; {"strain": "C57BL/6J", "age": "5m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "71"}
SRX21474998 Bone Marrow
0.779
9.8
39727
1116.4
489
949.5
1087
12041.7
0.980
title: WT addback in vivo 3A; {"strain": "C57BL/6J", "age": "4m", "dev_stage": "Adult", "collection_date": "not provided", "geo_loc_name": "not provided", "sex": "male", "tissue": "Bone marrow", "genotype": "Dnmt3a+/+", "replicate": "1", "sample_number": "72"}
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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