Mouse methylome studies ERP003907 Track Settings
Study title: Methylome_and_Hydroxymethylome_of_iPSCSRA: ERP003907 GEO: not foundPubmed: not found
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
ERX1246049 ERS822411
0.692
1.8
21671
2030.2
0
0.0
283
56651.9
0.992
title: Illumina HiSeq 2500 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-08T14:02:50Z", "ENA-LAST-UPDATE": "2018-03-09T04:10:29Z", "External_Id": "SAMEA3515262", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-08T14:02:50Z", "INSDC_last_update": "2018-03-09T04:10:29Z", "INSDC_status": "public", "Submitter_Id": "2769STDY6182410-sc-2382182", "common_name": "house mouse", "sample_name": "2769STDY6182410-sc-2382182", "scientific_name": "Mus musculus"}
ERX1246050 ERS822412
0.381
1.8
0
0.0
0
0.0
1
41725280.0
0.993
title: Illumina HiSeq 2500 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-08T14:02:50Z", "ENA-LAST-UPDATE": "2018-03-09T04:10:29Z", "External_Id": "SAMEA3515263", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-08T14:02:50Z", "INSDC_last_update": "2018-03-09T04:10:29Z", "INSDC_status": "public", "Submitter_Id": "2769STDY6182411-sc-2382183", "common_name": "house mouse", "sample_name": "2769STDY6182411-sc-2382183", "scientific_name": "Mus musculus"}
ERX1246056 ERS822412
0.382
1.7
3
613500.3
0
0.0
0
0.0
0.993
title: Illumina HiSeq 2500 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2015-12-08T14:02:50Z", "ENA-LAST-UPDATE": "2018-03-09T04:10:29Z", "External_Id": "SAMEA3515263", "INSDC_center_name": "SC", "INSDC_first_public": "2015-12-08T14:02:50Z", "INSDC_last_update": "2018-03-09T04:10:29Z", "INSDC_status": "public", "Submitter_Id": "2769STDY6182411-sc-2382183", "common_name": "house mouse", "sample_name": "2769STDY6182411-sc-2382183", "scientific_name": "Mus musculus"}
ERX371615 iPSC
0.608
2.7
25162
2075.2
0
0.0
532
42484.6
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189560", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC29_BS-sc-2013-09-18T12:30:24Z-1692910", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC29_BS-sc-2013-09-18T12:30:24Z-1692910", "scientific_name": "Mus musculus"}
ERX371616 iPSC
0.277
2.7
2
850454.5
0
0.0
0
0.0
0.997
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:42:53Z", "External_Id": "SAMEA2189559", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:42:53Z", "INSDC_status": "public", "Submitter_Id": "iPSC28_BS-sc-2013-09-18T12:30:17Z-1692909", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC28_BS-sc-2013-09-18T12:30:17Z-1692909", "scientific_name": "Mus musculus"}
ERX371617 iPSC
0.637
2.6
23770
1709.5
0
0.0
538
34189.3
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:42:53Z", "External_Id": "SAMEA2189554", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:42:53Z", "INSDC_status": "public", "Submitter_Id": "iPSC27_BS-sc-2013-09-18T12:28:40Z-1692908", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC27_BS-sc-2013-09-18T12:28:40Z-1692908", "scientific_name": "Mus musculus"}
ERX371618 iPSC
0.593
2.1
23029
2781.0
0
0.0
571
61797.4
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189557", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC29_oxBS-sc-2013-09-18T12:30:03Z-1692913", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC29_oxBS-sc-2013-09-18T12:30:03Z-1692913", "scientific_name": "Mus musculus"}
ERX371619 iPSC
0.262
2.1
1
730206.0
0
0.0
1
33790000.0
0.997
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189556", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC28_oxBS-sc-2013-09-18T12:29:53Z-1692912", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC28_oxBS-sc-2013-09-18T12:29:53Z-1692912", "scientific_name": "Mus musculus"}
ERX371620 iPSC
0.625
2.1
22200
2141.5
0
0.0
367
51320.3
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189555", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC27_oxBS-sc-2013-09-18T12:29:46Z-1692911", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC27_oxBS-sc-2013-09-18T12:29:46Z-1692911", "scientific_name": "Mus musculus"}
ERX371621 ESC
0.730
5.5
31315
1268.5
25
991.0
1806
14986.4
0.994
title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189552", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "TMBD10_BS-sc-2013-09-18T12:28:21Z-1692906", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "TMBD10_BS-sc-2013-09-18T12:28:21Z-1692906", "scientific_name": "Mus musculus"}
ERX371622 ESC
0.716
4.3
31698
1340.0
28
1129.8
1263
23330.6
0.994
title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189553", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "TMBD10_oxBS-sc-2013-09-18T12:28:31Z-1692907", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "TMBD10_oxBS-sc-2013-09-18T12:28:31Z-1692907", "scientific_name": "Mus musculus"}
ERX371623 iPSC
0.625
2.1
21129
2178.0
0
0.0
401
45059.4
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189566", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC38_BS-sc-2013-09-18T12:31:20Z-1692917", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC38_BS-sc-2013-09-18T12:31:20Z-1692917", "scientific_name": "Mus musculus"}
ERX371624 iPSC
0.647
2.1
22522
1923.6
0
0.0
239
50856.8
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:42:53Z", "External_Id": "SAMEA2189565", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:42:53Z", "INSDC_status": "public", "Submitter_Id": "iPSC37_BS-sc-2013-09-18T12:31:14Z-1692916", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC37_BS-sc-2013-09-18T12:31:14Z-1692916", "scientific_name": "Mus musculus"}
ERX371625 iPSC
0.560
1.8
20203
2083.3
1
568.0
0
0.0
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189564", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC20_BS-sc-2013-09-18T12:31:06Z-1692915", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC20_BS-sc-2013-09-18T12:31:06Z-1692915", "scientific_name": "Mus musculus"}
ERX371626 iPSC
0.640
1.9
22521
2165.8
0
0.0
353
63057.1
0.994
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189558", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC19_BS-sc-2013-09-18T12:30:10Z-1692914", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC19_BS-sc-2013-09-18T12:30:10Z-1692914", "scientific_name": "Mus musculus"}
ERX371627 iPSC
0.616
1.9
20843
2416.8
0
0.0
312
62697.8
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189563", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC38_oxBS-sc-2013-09-18T12:30:43Z-1692921", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC38_oxBS-sc-2013-09-18T12:30:43Z-1692921", "scientific_name": "Mus musculus"}
ERX371628 iPSC
0.637
1.9
21910
2165.8
0
0.0
350
55387.9
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:42:53Z", "External_Id": "SAMEA2189562", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:42:53Z", "INSDC_status": "public", "Submitter_Id": "iPSC37_oxBS-sc-2013-09-18T12:30:37Z-1692920", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC37_oxBS-sc-2013-09-18T12:30:37Z-1692920", "scientific_name": "Mus musculus"}
ERX371629 iPSC
0.552
1.7
20047
2096.0
1
674.0
0
0.0
0.997
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189561", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC20_oxBS-sc-2013-09-18T12:30:31Z-1692919", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC20_oxBS-sc-2013-09-18T12:30:31Z-1692919", "scientific_name": "Mus musculus"}
ERX371630 iPSC
0.626
1.8
21635
2473.1
0
0.0
497
70369.2
0.994
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189567", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "iPSC19_oxBS-sc-2013-09-18T12:31:26Z-1692918", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "iPSC19_oxBS-sc-2013-09-18T12:31:26Z-1692918", "scientific_name": "Mus musculus"}
ERX371631 MEF
0.620
3.5
26928
1582.9
0
0.0
330
23373.7
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:42:59Z", "External_Id": "SAMEA2189568", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:42:59Z", "INSDC_status": "public", "Submitter_Id": "pMEFWt_BS-sc-2013-09-18T12:31:34Z-1692922", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "pMEFWt_BS-sc-2013-09-18T12:31:34Z-1692922", "scientific_name": "Mus musculus"}
ERX371632 MEF
0.641
4.1
27428
1437.0
2
907.5
398
23093.3
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:43:34Z", "External_Id": "SAMEA2189569", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:43:34Z", "INSDC_status": "public", "Submitter_Id": "pMEFAIDKO_BS-sc-2013-09-18T12:31:41Z-1692923", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "pMEFAIDKO_BS-sc-2013-09-18T12:31:41Z-1692923", "scientific_name": "Mus musculus"}
ERX371633 MEF
0.614
3.1
24653
1794.6
0
0.0
286
26848.5
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:42:35Z", "External_Id": "SAMEA2189570", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:42:35Z", "INSDC_status": "public", "Submitter_Id": "pMEFWt_oxBS-sc-2013-09-18T12:31:48Z-1692924", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "pMEFWt_oxBS-sc-2013-09-18T12:31:48Z-1692924", "scientific_name": "Mus musculus"}
ERX371634 MEF
0.639
3.6
27083
1495.1
4
973.8
407
21962.9
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-01-07T10:46:12Z", "ENA-LAST-UPDATE": "2018-03-08T16:42:59Z", "External_Id": "SAMEA2189571", "INSDC_center_name": "SC", "INSDC_first_public": "2014-01-07T10:46:12Z", "INSDC_last_update": "2018-03-08T16:42:59Z", "INSDC_status": "public", "Submitter_Id": "pMEFAIDKO_oxBS-sc-2013-09-18T12:31:54Z-1692925", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "pMEFAIDKO_oxBS-sc-2013-09-18T12:31:54Z-1692925", "scientific_name": "Mus musculus"}
ERX502124 MEF
0.615
2.5
21569
2094.5
0
0.0
320
31663.7
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:44Z", "External_Id": "SAMEA2361784", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:44Z", "INSDC_status": "public", "Submitter_Id": "BSeq_MEF1-sc-1861756", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_MEF1-sc-1861756", "scientific_name": "Mus musculus"}
ERX502125 MEF
0.633
2.4
25943
1853.7
0
0.0
398
31181.0
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:44Z", "External_Id": "SAMEA2361785", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:44Z", "INSDC_status": "public", "Submitter_Id": "BSeq_MEF2-sc-1861757", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_MEF2-sc-1861757", "scientific_name": "Mus musculus"}
ERX502126 MEF
0.619
2.5
24259
1918.7
0
0.0
288
31985.3
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361786", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "BSeq_MEF3-sc-1861758", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_MEF3-sc-1861758", "scientific_name": "Mus musculus"}
ERX502127 ESC
0.635
2.5
25540
1721.2
0
0.0
331
42929.1
0.994
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361787", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "BSeq_TMBD1-sc-1861759", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_TMBD1-sc-1861759", "scientific_name": "Mus musculus"}
ERX502128 ESC
0.665
2.2
23430
1646.6
0
0.0
410
39782.9
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361788", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "BSeq_TMBD2-sc-1861760", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_TMBD2-sc-1861760", "scientific_name": "Mus musculus"}
ERX502129 ESC
0.661
2.5
24822
1547.8
1
1733.0
312
38651.4
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361789", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "BSeq_TMBD3-sc-1861761", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_TMBD3-sc-1861761", "scientific_name": "Mus musculus"}
ERX502130 MEF
0.609
2.3
20908
2289.3
0
0.0
198
43181.9
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361790", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_MEF1-sc-1861762", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_MEF1-sc-1861762", "scientific_name": "Mus musculus"}
ERX502131 MEF
0.628
2.3
23705
1993.3
0
0.0
344
36251.8
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361791", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_MEF2-sc-1861763", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_MEF2-sc-1861763", "scientific_name": "Mus musculus"}
ERX502132 MEF
0.617
2.4
22875
2032.8
0
0.0
318
30661.2
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361792", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_MEF3-sc-1861764", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_MEF3-sc-1861764", "scientific_name": "Mus musculus"}
ERX502133 ESC
0.627
2.1
23572
2031.1
0
0.0
366
56212.7
0.994
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361793", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_TMBD1-sc-1861765", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_TMBD1-sc-1861765", "scientific_name": "Mus musculus"}
ERX502134 ESC
0.653
2.2
24508
1662.7
1
1097.0
448
39933.2
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361794", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_TMBD2-sc-1861766", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_TMBD2-sc-1861766", "scientific_name": "Mus musculus"}
ERX502135 ESC
0.648
2.3
24402
1691.6
2
968.5
457
41356.1
0.995
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361795", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_TMBD3-sc-1861767", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_TMBD3-sc-1861767", "scientific_name": "Mus musculus"}
ERX502136 iPSC
0.596
2.2
19882
3084.5
0
0.0
424
1773914.8
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361796", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "BSeq_T_S_Exp10-sc-1861768", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_T_S_Exp10-sc-1861768", "scientific_name": "Mus musculus"}
ERX502137 iPSC
0.600
2.3
19764
2637.5
0
0.0
160
57899.2
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361798", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "BSeq_T_S_Exp11-sc-1861770", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_T_S_Exp11-sc-1861770", "scientific_name": "Mus musculus"}
ERX502138 iPSC
0.591
2.3
19440
3172.1
0
0.0
513
1489791.6
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:53Z", "External_Id": "SAMEA2361800", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:53Z", "INSDC_status": "public", "Submitter_Id": "BSeq_T_S_Exp16-sc-1861772", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_T_S_Exp16-sc-1861772", "scientific_name": "Mus musculus"}
ERX502139 iPSC
0.565
2.2
18683
3640.9
1
928.0
533
1313128.5
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:45Z", "External_Id": "SAMEA2361797", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:45Z", "INSDC_status": "public", "Submitter_Id": "BSeq_T_S_Exp10-sc-1861769", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_T_S_Exp10-sc-1861769", "scientific_name": "Mus musculus"}
ERX502140 iPSC
0.578
2.2
18639
3127.8
0
0.0
745
445530.1
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:53Z", "External_Id": "SAMEA2361799", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:53Z", "INSDC_status": "public", "Submitter_Id": "BSeq_T_S_Exp11-sc-1861771", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_T_S_Exp11-sc-1861771", "scientific_name": "Mus musculus"}
ERX502141 iPSC
0.569
2.1
18291
3635.4
0
0.0
521
1354801.7
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361801", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "BSeq_T_S_Exp16-sc-1861773", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_T_S_Exp16-sc-1861773", "scientific_name": "Mus musculus"}
ERX502142 iPSC
0.591
2.1
19180
3127.5
0
0.0
373
1875856.4
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:53Z", "External_Id": "SAMEA2361802", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:53Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_T_S_Exp10-sc-1861774", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "oxBSeq_T_S_Exp10-sc-1861774", "scientific_name": "Mus musculus"}
ERX502143 iPSC
0.597
2.1
19163
2779.1
0
0.0
108
82896.6
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361804", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_T_S_Exp11-sc-1861776", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "oxBSeq_T_S_Exp11-sc-1861776", "scientific_name": "Mus musculus"}
ERX502144 iPSC
0.588
2.3
19200
3203.0
0
0.0
489
1531601.1
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:53Z", "External_Id": "SAMEA2361806", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:53Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_T_S_Exp16-sc-1861778", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "oxBSeq_T_S_Exp16-sc-1861778", "scientific_name": "Mus musculus"}
ERX502145 iPSC
0.555
2.2
18193
3623.3
1
901.0
560
1205334.1
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:53Z", "External_Id": "SAMEA2361803", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:53Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_T_S_Exp10-sc-1861775", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "oxBSeq_T_S_Exp10-sc-1861775", "scientific_name": "Mus musculus"}
ERX502146 iPSC
0.566
2.2
18298
3229.7
1
584.0
383
165477.1
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:53Z", "External_Id": "SAMEA2361805", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:53Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_T_S_Exp11-sc-1861777", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "oxBSeq_T_S_Exp11-sc-1861777", "scientific_name": "Mus musculus"}
ERX502147 iPSC
0.557
2.2
18464
3713.7
0
0.0
562
1208502.1
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361807", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_T_S_Exp16-sc-1861779", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "oxBSeq_T_S_Exp16-sc-1861779", "scientific_name": "Mus musculus"}
ERX502151 iPSC
0.393
1.5
1
655133.0
0
0.0
21
9304185.1
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:45Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:53Z", "External_Id": "SAMEA2361811", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:45Z", "INSDC_last_update": "2018-03-08T17:11:53Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P8_iPSC67-sc-1861783", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_P8_iPSC67-sc-1861783", "scientific_name": "Mus musculus"}
ERX502153 iPSC
0.431
1.5
1
672916.0
0
0.0
96
213249.2
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-06-16T11:43:44Z", "ENA-LAST-UPDATE": "2018-03-08T17:11:54Z", "External_Id": "SAMEA2361813", "INSDC_center_name": "SC", "INSDC_first_public": "2014-06-16T11:43:44Z", "INSDC_last_update": "2018-03-08T17:11:54Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P8_iPSC73-sc-1861785", "common_name": "house mouse", "description": "DNA from iPSC", "sample_name": "BSeq_P8_iPSC73-sc-1861785", "scientific_name": "Mus musculus"}
ERX622633 MEF
0.195
1.5
1
631824.0
0
0.0
1
109669217.0
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:48Z", "External_Id": "SAMEA2633691", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T19:03:48Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC44-sc-2014730", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_P29_iPSC44-sc-2014730", "scientific_name": "Mus musculus"}
ERX622635 MEF
0.554
1.6
22734
2953.7
0
0.0
441
102173.3
0.997
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T20:10:43Z", "External_Id": "SAMEA2633693", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T20:10:43Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC66-sc-2014732", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_P29_iPSC66-sc-2014732", "scientific_name": "Mus musculus"}
ERX622636 ESC
0.443
1.4
0
0.0
0
0.0
241
198054.5
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:49Z", "External_Id": "SAMEA2633694", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T19:03:49Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC67-sc-2014733", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_P29_iPSC67-sc-2014733", "scientific_name": "Mus musculus"}
ERX622637 ESC
0.562
1.5
23406
2275.7
0
0.0
200
110536.4
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633695", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC72-sc-2014734", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_P29_iPSC72-sc-2014734", "scientific_name": "Mus musculus"}
ERX622638 ESC
0.277
1.5
0
0.0
0
0.0
745
1648693.8
1.000
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T20:10:43Z", "External_Id": "SAMEA2633696", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T20:10:43Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC73-sc-2014735", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_P29_iPSC73-sc-2014735", "scientific_name": "Mus musculus"}
ERX625586 MEF
0.188
1.5
1
714527.0
0
0.0
0
0.0
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:49Z", "External_Id": "SAMEA2633697", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:03:49Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC44-sc-2014736", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_P29_iPSC44-sc-2014736", "scientific_name": "Mus musculus"}
ERX625587 MEF
0.267
1.6
1
838820.0
0
0.0
5
18725852.8
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633698", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC45-sc-2014737", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_P29_iPSC45-sc-2014737", "scientific_name": "Mus musculus"}
ERX625588 MEF
0.540
1.5
23884
3127.2
1
564.0
475
118367.9
0.997
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633702", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC66-sc-2014738", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_P29_iPSC66-sc-2014738", "scientific_name": "Mus musculus"}
ERX625589 ESC
0.424
1.5
2
642479.5
0
0.0
467
190628.7
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T20:10:43Z", "External_Id": "SAMEA2633699", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T20:10:43Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC67-sc-2014739", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_P29_iPSC67-sc-2014739", "scientific_name": "Mus musculus"}
ERX625590 ESC
0.552
1.5
23915
2398.2
0
0.0
299
111413.6
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:49Z", "External_Id": "SAMEA2633700", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:03:49Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC72-sc-2014740", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_P29_iPSC72-sc-2014740", "scientific_name": "Mus musculus"}
ERX625591 ESC
0.276
1.6
0
0.0
0
0.0
803
1550549.9
1.000
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633701", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC73-sc-2014741", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_P29_iPSC73-sc-2014741", "scientific_name": "Mus musculus"}
ERX634528 MEF
0.190
2.4
2
877087.0
0
0.0
0
0.0
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:48Z", "External_Id": "SAMEA2633691", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T19:03:48Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC44-sc-2014730", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_P29_iPSC44-sc-2014730", "scientific_name": "Mus musculus"}
ERX634529 MEF
0.274
2.2
2
857164.5
0
0.0
6
12285332.5
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633692", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC45-sc-2014731", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_P29_iPSC45-sc-2014731", "scientific_name": "Mus musculus"}
ERX634530 MEF
0.547
2.5
22331
3147.0
0
0.0
494
53685.6
0.997
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T20:10:43Z", "External_Id": "SAMEA2633693", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T20:10:43Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC66-sc-2014732", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "BSeq_P29_iPSC66-sc-2014732", "scientific_name": "Mus musculus"}
ERX634531 ESC
0.436
2.3
1671
16184.4
1
670.0
576
74617.0
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:49Z", "External_Id": "SAMEA2633694", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T19:03:49Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC67-sc-2014733", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_P29_iPSC67-sc-2014733", "scientific_name": "Mus musculus"}
ERX634532 ESC
0.554
2.3
21739
2775.3
0
0.0
450
41219.6
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633695", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC72-sc-2014734", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_P29_iPSC72-sc-2014734", "scientific_name": "Mus musculus"}
ERX634533 ESC
0.266
2.4
0
0.0
0
0.0
977
1321603.5
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-04T16:18:36Z", "ENA-LAST-UPDATE": "2018-03-08T20:10:43Z", "External_Id": "SAMEA2633696", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-04T16:18:36Z", "INSDC_last_update": "2018-03-08T20:10:43Z", "INSDC_status": "public", "Submitter_Id": "BSeq_P29_iPSC73-sc-2014735", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "BSeq_P29_iPSC73-sc-2014735", "scientific_name": "Mus musculus"}
ERX634534 MEF
0.183
2.1
1
915240.0
0
0.0
0
0.0
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:49Z", "External_Id": "SAMEA2633697", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:03:49Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC44-sc-2014736", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_P29_iPSC44-sc-2014736", "scientific_name": "Mus musculus"}
ERX634535 MEF
0.261
2.3
2
965308.5
0
0.0
12
7710416.1
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633698", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC45-sc-2014737", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_P29_iPSC45-sc-2014737", "scientific_name": "Mus musculus"}
ERX634536 MEF
0.531
2.2
22657
3544.2
0
0.0
388
81681.9
0.997
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633702", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC66-sc-2014738", "common_name": "house mouse", "description": "DNA from MEF", "sample_name": "oxBSeq_P29_iPSC66-sc-2014738", "scientific_name": "Mus musculus"}
ERX634537 ESC
0.416
2.1
0
0.0
2
716.5
442
115631.1
0.998
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T20:10:43Z", "External_Id": "SAMEA2633699", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T20:10:43Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC67-sc-2014739", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_P29_iPSC67-sc-2014739", "scientific_name": "Mus musculus"}
ERX634538 ESC
0.543
2.1
22294
2927.2
1
502.0
464
54450.5
0.996
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:03:49Z", "External_Id": "SAMEA2633700", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:03:49Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC72-sc-2014740", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_P29_iPSC72-sc-2014740", "scientific_name": "Mus musculus"}
ERX634539 ESC
0.267
2.4
0
0.0
0
0.0
978
1313523.4
0.999
title: Illumina HiSeq 2000 paired end sequencing; {"sex": "female", "ArrayExpress-Species": "Mus Musculus", "ENA-CHECKLIST": "ERC000011", "ENA-FIRST-PUBLIC": "2014-11-11T09:56:56Z", "ENA-LAST-UPDATE": "2018-03-08T19:48:11Z", "External_Id": "SAMEA2633701", "INSDC_center_name": "SC", "INSDC_first_public": "2014-11-11T09:56:56Z", "INSDC_last_update": "2018-03-08T19:48:11Z", "INSDC_status": "public", "Submitter_Id": "oxBSeq_P29_iPSC73-sc-2014741", "common_name": "house mouse", "description": "DNA from ESC", "sample_name": "oxBSeq_P29_iPSC73-sc-2014741", "scientific_name": "Mus musculus"}
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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