Human methylome studies SRP462543 Track Settings
Study title: iPSC-based modeling of preeclampsia identifies defects in extravillous trophoblast differentiationSRA: SRP462543 GEO: not foundPubmed: not found
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
SRX21852585 Placenta
0.371
9.0
64040
18353.5
352
1009.7
4995
257234.1
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast; {"isolate": "1048", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 1", "cell_line": "1048", "cell_subtype": "primary", "cell_type": "EVT", "disease": "control", "sample_type": "tissue sample"}
SRX21852586 Placenta
0.375
11.5
73144
16575.7
462
1003.7
6912
185869.0
0.982
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast; {"isolate": "1048", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 2", "cell_line": "1048", "cell_subtype": "primary", "cell_type": "EVT", "disease": "control", "sample_type": "tissue sample"}
SRX21852587 Placenta
0.298
4.6
10646
51257.1
29
980.9
3311
372189.9
0.980
title: WGBS of homo sapiens trophoblast stem cell; {"isolate": "1276C", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 1", "cell_line": "1276C", "cell_subtype": "primary", "cell_type": "hTSC", "disease": "control", "sample_type": "tissue sample"}
SRX21852588 Placenta
0.297
6.0
29802
29179.6
89
911.6
3765
326416.4
0.980
title: WGBS of homo sapiens trophoblast stem cell; {"isolate": "1276C", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 2", "cell_line": "1276C", "cell_subtype": "primary", "cell_type": "hTSC", "disease": "control", "sample_type": "tissue sample"}
SRX21852589 iPSC derived extravillous trophoblast
0.387
15.8
55169
17356.5
508
927.0
4437
309173.6
0.982
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1754", "cell_subtype": "naive", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852590 iPSC derived extravillous trophoblast
0.388
12.4
48383
18891.7
380
883.8
4111
331424.5
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1754", "cell_subtype": "naive", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852591 iPSC derived trophoblast stem cell
0.402
29.4
75938
14434.0
604
890.8
5282
263376.3
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1754", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852592 iPSC derived trophoblast stem cell
0.405
20.2
66656
15862.7
457
908.0
4993
278002.6
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1754", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852593 iSPC reprogrammed from mesenchymal stem cell
0.409
13.1
64466
8771.0
98
952.7
5212
147304.4
0.979
title: WGBS of homo sapiens naive iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1754", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852594 iSPC reprogrammed from mesenchymal stem cell
0.407
11.6
62821
9028.0
75
835.4
5098
148679.8
0.979
title: WGBS of homo sapiens naive iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1754", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852595 iPSC derived extravillous trophoblast
0.649
11.9
61444
4618.6
313
1072.2
2343
478622.7
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1754", "cell_subtype": "prime", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852596 iPSC derived extravillous trophoblast
0.647
9.3
57987
4612.1
238
1088.9
1921
586953.4
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1754", "cell_subtype": "prime", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852597 Placenta
0.320
10.6
68940
17444.7
451
1000.1
5091
250722.7
0.981
title: WGBS of homo sapiens trophoblast stem cell; {"isolate": "1048", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 1", "cell_line": "1048", "cell_subtype": "primary", "cell_type": "hTSC", "disease": "control", "sample_type": "tissue sample"}
SRX21852598 iPSC derived trophoblast stem cell
0.584
13.3
61154
4683.0
346
1055.7
2377
436343.5
0.982
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1754", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852599 iPSC derived trophoblast stem cell
0.582
11.8
57850
4817.1
346
1086.7
2309
450141.3
0.981
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1754", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852600 iSPC reprogrammed from mesenchymal stem cell
0.815
10.3
33158
1302.8
253
1177.3
1942
12796.6
0.973
title: WGBS of homo sapiens primed iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1754", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852601 iSPC reprogrammed from mesenchymal stem cell
0.795
10.5
33461
1273.9
288
1147.6
1913
12146.1
0.973
title: WGBS of homo sapiens primed iPSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1754", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852602 Mesenchymal Stem Cell
0.696
8.4
54969
2224.3
75
1311.2
1738
549185.3
0.982
title: WGBS of homo sapiens MSC; {"isolate": "1754", "age": "39 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "Mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1754", "cell_subtype": "primary", "cell_type": "MSC", "disease": "control", "sample_type": "cell culture"}
SRX21852603 iPSC derived extravillous trophoblast
0.399
10.4
46356
20506.2
185
881.1
4046
332666.7
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1932", "cell_subtype": "naive", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852604 iPSC derived extravillous trophoblast
0.401
11.3
49171
19807.6
230
876.4
4690
286639.1
0.982
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1932", "cell_subtype": "naive", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852605 iPSC derived trophoblast stem cell
0.392
14.4
59019
17651.7
347
865.3
5060
265934.0
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1932", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852606 iPSC derived trophoblast stem cell
0.389
16.5
63788
16774.7
426
874.6
5220
258554.6
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1932", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852607 iSPC reprogrammed from mesenchymal stem cell
0.446
8.9
56002
7255.7
34
950.9
2850
259771.1
0.977
title: WGBS of homo sapiens naive iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1932", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852608 Placenta
0.321
12.3
73926
16491.8
547
1017.6
6923
185013.4
0.981
title: WGBS of homo sapiens trophoblast stem cell; {"isolate": "1048", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 2", "cell_line": "1048", "cell_subtype": "primary", "cell_type": "hTSC", "disease": "control", "sample_type": "tissue sample"}
SRX21852609 iSPC reprogrammed from mesenchymal stem cell
0.442
8.4
53580
6956.6
35
858.8
2830
252715.6
0.977
title: WGBS of homo sapiens naive iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1932", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852610 iPSC derived extravillous trophoblast
0.561
4.5
38068
17396.1
39
1342.2
2244
528557.6
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1932", "cell_subtype": "prime", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852611 iPSC derived extravillous trophoblast
0.562
11.2
55699
13987.1
512
1163.5
3589
331197.7
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1932", "cell_subtype": "prime", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852612 iPSC derived trophoblast stem cell
0.494
16.5
58632
12309.2
647
1168.2
3404
338170.7
0.982
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1932", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852613 iPSC derived trophoblast stem cell
0.494
10.3
50128
13882.8
382
1208.9
2665
438988.6
0.982
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1932", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852614 iSPC reprogrammed from mesenchymal stem cell
0.821
12.0
38095
1162.6
780
1294.6
4122
13112.4
0.976
title: WGBS of homo sapiens primed iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1932", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852615 iSPC reprogrammed from mesenchymal stem cell
0.819
12.6
38709
1152.5
841
1289.5
4248
12755.5
0.975
title: WGBS of homo sapiens primed iPSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1932", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852616 iPSC derived trophoblast stem cell
0.582
9.2
53041
5832.5
512
1167.1
1572
728455.9
0.981
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1981", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852617 iPSC derived trophoblast stem cell
0.581
10.9
56354
5827.3
626
1135.5
1522
746772.6
0.981
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1981", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852618 iSPC reprogrammed from mesenchymal stem cell
0.807
10.6
35585
1199.2
632
1198.2
2211
22203.8
0.975
title: WGBS of homo sapiens primed iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1981", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852619 iSPC reprogrammed from mesenchymal stem cell
0.804
10.0
35192
1208.8
577
1217.8
2319
19949.5
0.975
title: WGBS of homo sapiens primed iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1981", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852620 Mesenchymal Stem Cell
0.690
10.4
67727
4409.7
283
1201.8
1773
579238.6
0.981
title: WGBS of homo sapiens MSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "Mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1981", "cell_subtype": "primary", "cell_type": "MSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852621 Placenta
0.376
9.6
65192
17634.0
374
987.9
5035
246898.0
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast; {"isolate": "1276C", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 2", "cell_line": "1276C", "cell_subtype": "primary", "cell_type": "EVT", "disease": "control", "sample_type": "tissue sample"}
SRX21852622 Mesenchymal Stem Cell
0.697
12.7
63029
2385.7
340
1168.2
2062
437848.1
0.982
title: WGBS of homo sapiens MSC; {"isolate": "1932", "age": "32 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "Mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1932", "cell_subtype": "primary", "cell_type": "MSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852623 iPSC derived extravillous trophoblast
0.409
13.5
55795
18522.8
277
850.9
5092
272227.9
0.982
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1933", "cell_subtype": "naive", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852624 iPSC derived extravillous trophoblast
0.407
10.0
44748
21329.4
159
895.4
4136
335563.9
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1933", "cell_subtype": "naive", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852625 Placenta
0.337
3.9
11074
52676.2
34
964.1
3609
370516.4
0.980
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast; {"isolate": "1049", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 1", "cell_line": "1049", "cell_subtype": "primary", "cell_type": "EVT", "disease": "control", "sample_type": "tissue sample"}
SRX21852626 iPSC derived trophoblast stem cell
0.382
10.9
49679
20177.8
188
803.1
4183
333065.4
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1933", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852627 iPSC derived trophoblast stem cell
0.384
10.5
48320
20533.7
222
822.2
4167
332995.4
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1933", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852628 iSPC reprogrammed from mesenchymal stem cell
0.416
12.9
62258
8130.2
76
864.6
4531
155905.1
0.978
title: WGBS of homo sapiens naive iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1933", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852629 iSPC reprogrammed from mesenchymal stem cell
0.415
11.2
59993
8324.0
65
859.9
3403
212205.0
0.978
title: WGBS of homo sapiens naive iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1933", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852630 iPSC derived extravillous trophoblast
0.561
9.5
50158
14964.5
159
1056.1
2988
426147.3
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1933", "cell_subtype": "prime", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852631 iPSC derived extravillous trophoblast
0.562
8.4
48099
15217.8
138
1087.2
2876
437635.4
0.980
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1933", "cell_subtype": "prime", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852632 iPSC derived trophoblast stem cell
0.513
15.2
57935
12971.5
302
975.7
3334
366297.7
0.982
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1933", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852633 iPSC derived trophoblast stem cell
0.511
12.5
53834
13598.0
226
1048.8
3180
379550.0
0.982
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1933", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852634 iSPC reprogrammed from mesenchymal stem cell
0.823
5.7
32899
1320.8
93
1111.0
1209
21497.1
0.975
title: WGBS of homo sapiens primed iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1933", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852635 iSPC reprogrammed from mesenchymal stem cell
0.820
6.0
33281
1304.1
108
1092.0
1366
20571.0
0.974
title: WGBS of homo sapiens primed iPSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1933", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852636 Placenta
0.337
4.8
22864
36219.5
58
984.9
3804
349595.3
0.980
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast; {"isolate": "1049", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 2", "cell_line": "1049", "cell_subtype": "primary", "cell_type": "EVT", "disease": "control", "sample_type": "tissue sample"}
SRX21852637 Mesenchymal Stem Cell
0.660
12.2
68700
4401.9
123
1139.5
2215
456648.2
0.982
title: WGBS of homo sapiens MSC; {"isolate": "1933", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "Mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1933", "cell_subtype": "primary", "cell_type": "MSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852638 iPSC derived extravillous trophoblast
0.419
5.5
19799
30138.9
54
1041.0
2567
477511.3
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "AN1", "age": "35 years old", "biomaterial_provider": "Thorold Theunissen", "collection_date": "2020", "geo_loc_name": "USA: MO, St. Louis", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "AN1", "cell_subtype": "naive", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852639 iPSC derived extravillous trophoblast
0.422
13.1
54618
16383.1
476
917.9
3891
315270.6
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "AN1", "age": "35 years old", "biomaterial_provider": "Thorold Theunissen", "collection_date": "2020", "geo_loc_name": "USA: MO, St. Louis", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "AN1", "cell_subtype": "naive", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852640 iPSC derived trophoblast stem cell
0.424
12.7
54004
16689.9
412
963.0
4032
304789.1
0.980
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "AN1", "age": "35 years old", "biomaterial_provider": "Thorold Theunissen", "collection_date": "2020", "geo_loc_name": "USA: MO, St. Louis", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "AN1", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852641 iPSC derived trophoblast stem cell
0.422
10.3
48440
17952.9
337
939.3
3248
381272.1
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "AN1", "age": "35 years old", "biomaterial_provider": "Thorold Theunissen", "collection_date": "2020", "geo_loc_name": "USA: MO, St. Louis", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "AN1", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852642 iPSC reprogrammed from renal epithelial
0.480
9.1
51422
4904.2
92
836.9
2788
244934.2
0.976
title: WGBS of homo sapiens naive iPSC; {"isolate": "AN1", "age": "35 years old", "biomaterial_provider": "Thorold Theunissen", "collection_date": "2020", "geo_loc_name": "USA: MO, St. Louis", "sex": "female", "tissue": "iPSC reprogrammed from renal epithelial cells", "replicate": "biological replicate 1", "cell_line": "AN1", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852643 iPSC reprogrammed from renal epithelial
0.479
10.8
56458
5307.1
811
853.7
2697
257846.2
0.977
title: WGBS of homo sapiens naive iPSC; {"isolate": "AN1", "age": "35 years old", "biomaterial_provider": "Thorold Theunissen", "collection_date": "2020", "geo_loc_name": "USA: MO, St. Louis", "sex": "female", "tissue": "iPSC reprogrammed from renal epithelial cells", "replicate": "biological replicate 2", "cell_line": "AN1", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852644 iPSC derived extravillous trophoblast
0.553
10.8
55100
13307.1
193
1134.2
3329
353760.1
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1938", "age": "26 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1938", "cell_subtype": "prime", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852645 iPSC derived extravillous trophoblast
0.551
7.2
45542
15016.1
86
1088.9
2756
433987.9
0.980
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1938", "age": "26 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1938", "cell_subtype": "prime", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852646 iPSC derived trophoblast stem cell
0.493
5.8
30816
18614.4
57
1310.6
2221
532540.5
0.981
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1938", "age": "26 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1938", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852647 Placenta
0.290
8.8
55219
21156.7
223
1013.1
5808
226108.6
0.982
title: WGBS of homo sapiens trophoblast stem cell; {"isolate": "1049", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 1", "cell_line": "1049", "cell_subtype": "primary", "cell_type": "hTSC", "disease": "control", "sample_type": "tissue sample"}
SRX21852648 iPSC derived trophoblast stem cell
0.491
8.7
44678
14979.8
142
1171.0
2568
460582.6
0.981
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1938", "age": "26 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1938", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852649 iSPC reprogrammed from mesenchymal stem cell
0.814
10.0
35105
1243.4
303
1202.4
1992
13471.8
0.974
title: WGBS of homo sapiens primed iPSC; {"isolate": "1938", "age": "26 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1938", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852650 iSPC reprogrammed from mesenchymal stem cell
0.818
11.7
36377
1211.7
337
1208.5
4005
8113.4
0.974
title: WGBS of homo sapiens primed iPSC; {"isolate": "1938", "age": "26 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1938", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852651 Mesenchymal Stem Cell
0.673
12.1
66090
3323.8
111
1194.7
2273
427032.5
0.981
title: WGBS of homo sapiens MSC; {"isolate": "1938", "age": "26 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "male", "tissue": "Mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1938", "cell_subtype": "primary", "cell_type": "MSC", "disease": "control", "sample_type": "cell culture"}
SRX21852652 iPSC derived extravillous trophoblast
0.396
10.6
59733
19307.3
314
909.5
3910
359698.0
0.978
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1947", "cell_subtype": "naive", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852653 iPSC derived extravillous trophoblast
0.399
12.8
63861
18525.4
4156
899.3
4655
301417.0
0.978
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1947", "cell_subtype": "naive", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852654 iPSC derived trophoblast stem cell
0.346
10.1
52933
19989.1
240
934.6
3532
391012.6
0.980
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1947", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852655 iPSC derived trophoblast stem cell
0.348
10.8
55420
19363.8
259
960.0
3613
383598.5
0.979
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1947", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852657 iSPC reprogrammed from mesenchymal stem cell
0.351
11.0
58777
10370.1
28
911.9
4655
172374.9
0.979
title: WGBS of homo sapiens naive iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1947", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852658 Placenta
0.288
10.2
61998
19462.2
387
978.9
5954
220519.0
0.982
title: WGBS of homo sapiens trophoblast stem cell; {"isolate": "1049", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 2", "cell_line": "1049", "cell_subtype": "primary", "cell_type": "hTSC", "disease": "control", "sample_type": "tissue sample"}
SRX21852659 iPSC derived extravillous trophoblast
0.589
6.7
47692
12149.9
118
1108.8
2117
589383.8
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1947", "cell_subtype": "prime", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852660 iPSC derived extravillous trophoblast
0.585
5.6
44030
12530.5
81
1048.9
1867
670121.9
0.980
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1947", "cell_subtype": "prime", "cell_type": "EVT", "disease": "control", "sample_type": "cell culture"}
SRX21852661 iPSC derived trophoblast stem cell
0.527
6.4
39395
13370.8
121
1063.0
1812
667214.9
0.981
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1947", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852662 iPSC derived trophoblast stem cell
0.528
8.8
49128
11644.1
216
1066.2
2029
593338.5
0.982
title: WGBS of homo sapiens trophoblast stem cell from primed iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1947", "cell_subtype": "prime", "cell_type": "hTSC", "disease": "control", "sample_type": "cell culture"}
SRX21852664 iSPC reprogrammed from mesenchymal stem cell
0.812
9.8
37050
1215.3
448
1144.3
2327
15833.2
0.976
title: WGBS of homo sapiens primed iPSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1947", "cell_subtype": "prime", "cell_type": "iPSC", "disease": "control", "sample_type": "cell culture"}
SRX21852665 Mesenchymal Stem Cell
0.680
12.5
59027
2108.7
305
1127.6
2054
438573.1
0.981
title: WGBS of homo sapiens MSC; {"isolate": "1947", "age": "34 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "Mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1947", "cell_subtype": "primary", "cell_type": "MSC", "disease": "control", "sample_type": "cell culture"}
SRX21852666 iPSC derived extravillous trophoblast
0.425
12.4
54868
15201.6
354
875.2
3857
304407.0
0.982
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1981", "cell_subtype": "naive", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852667 iPSC derived extravillous trophoblast
0.426
11.3
52320
15690.7
276
883.7
3760
311597.9
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from naive iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1981", "cell_subtype": "naive", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852668 iPSC derived trophoblast stem cell
0.409
30.1
73585
12670.5
715
885.7
4514
261413.6
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 1", "cell_line": "1981", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852669 Placenta
0.375
9.1
63421
18006.7
377
953.3
4963
250286.6
0.980
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast; {"isolate": "1276C", "age": "6 weeks (GA)", "biomaterial_provider": "Mana Parast", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "placenta", "replicate": "biological replicate 1", "cell_line": "1276C", "cell_subtype": "primary", "cell_type": "EVT", "disease": "control", "sample_type": "tissue sample"}
SRX21852670 iPSC derived trophoblast stem cell
0.410
16.5
61907
14371.2
498
890.8
4229
278291.2
0.982
title: WGBS of homo sapiens trophoblast stem cell from naive iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived trophoblast stem cell", "replicate": "biological replicate 2", "cell_line": "1981", "cell_subtype": "naive", "cell_type": "hTSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852671 iSPC reprogrammed from mesenchymal stem cell
0.499
14.4
55566
2877.3
105
938.9
4860
92531.8
0.977
title: WGBS of homo sapiens naive iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 1", "cell_line": "1981", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852672 iSPC reprogrammed from mesenchymal stem cell
0.510
19.9
58679
2743.7
177
865.7
5129
91029.3
0.977
title: WGBS of homo sapiens naive iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iSPC reprogrammed from mesenchymal stem cell", "replicate": "biological replicate 2", "cell_line": "1981", "cell_subtype": "naive", "cell_type": "iPSC", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852673 iPSC derived extravillous trophoblast
0.635
10.2
58547
5564.4
596
1153.3
1666
725503.9
0.982
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 1", "cell_line": "1981", "cell_subtype": "prime", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
SRX21852674 iPSC derived extravillous trophoblast
0.642
11.1
60128
5233.5
611
1171.4
1925
615599.4
0.981
title: WGBS of homo sapiens in vitro differentiated extravillous trophoblast from primed iPSC; {"isolate": "1981", "age": "33 weeks (GA)", "biomaterial_provider": "Mariko Horii", "collection_date": "2020", "geo_loc_name": "USA: California, San Diego", "sex": "female", "tissue": "iPSC derived extravillous trophoblast", "replicate": "biological replicate 2", "cell_line": "1981", "cell_subtype": "prime", "cell_type": "EVT", "disease": "preeclamptic", "sample_type": "cell culture"}
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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