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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005070
|DRA_sample_Accession=CAGE@SAMD00005070
|accession_numbers=CAGE;DRX008916;DRR009790;DRZ001215;DRZ002598
|accession_numbers=CAGE;DRX008916;DRR009790;DRZ001215;DRZ002598;DRZ012565;DRZ013948
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0000358,UBERON:0000307
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0000358,UBERON:0000307
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000349,CL:0000255,CL:0000034,CL:0000351
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000349,CL:0000255,CL:0000034,CL:0000351

Revision as of 22:06, 10 August 2017


Name:trophoblast stem cell line B1 differentiation
Species:Mouse (Mus musculus)
Library ID:CNhs13526
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationHirohiko Kodeki(RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB1 +d0
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005070
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13526 CAGE DRX008916 DRR009790
Accession ID Mm9

Library idBAMCTSS
CNhs13526 DRZ001215 DRZ002598
Accession ID Mm10

Library idBAMCTSS
CNhs13526 DRZ012565 DRZ013948
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs13526

00
10
100
1000
10000
1001-0.0356
1002-0.102
1003-0.175
10040
1005-0.294
1006-0.147
1007-0.115
10080
1009-0.161
1010.333
10100
1011-0.178
10120
1013-0.153
1014-0.0874
1015-0.132
1016-0.292
10170
10180.736
10190
1020
10200.222
10210.111
1022-0.0704
10230
1024-0.14
10250
10260
1027-0.048
10280
1029-0.115
103-0.0861
10300
1031-0.508
1032-0.293
10330
10340
10350
10360.105
10370
1038-0.112
1039-0.189
1040
1040-0.0865
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13526

Jaspar motifP-value
MA0002.20.253
MA0003.10.663
MA0004.10.126
MA0006.10.987
MA0007.10.861
MA0009.10.34
MA0014.10.0931
MA0017.10.981
MA0018.20.00345
MA0019.10.679
MA0024.11.00463e-4
MA0025.10.7
MA0027.10.789
MA0028.17.57934e-7
MA0029.10.00397
MA0030.10.659
MA0031.10.3
MA0035.20.391
MA0038.10.635
MA0039.28.12767e-6
MA0040.10.755
MA0041.10.163
MA0042.10.43
MA0043.10.00229
MA0046.13.94587e-11
MA0047.20.0219
MA0048.10.0303
MA0050.10.0386
MA0051.10.809
MA0052.11.28317e-4
MA0055.11.04279e-5
MA0057.10.978
MA0058.10.0616
MA0059.10.0185
MA0060.13.00502e-5
MA0061.10.54
MA0062.22.96043e-9
MA0065.20.288
MA0066.10.942
MA0067.10.306
MA0068.10.00324
MA0069.10.551
MA0070.10.402
MA0071.10.053
MA0072.10.495
MA0073.10.609
MA0074.10.775
MA0076.14.17421e-6
MA0077.10.369
MA0078.10.176
MA0079.20.193
MA0080.20.198
MA0081.10.796
MA0083.12.47107e-5
MA0084.10.616
MA0087.10.606
MA0088.10.161
MA0090.10.3
MA0091.10.953
MA0092.10.33
MA0093.10.118
MA0099.25.37098e-8
MA0100.10.0253
MA0101.10.154
MA0102.20.835
MA0103.10.0555
MA0104.20.0212
MA0105.10.172
MA0106.10.0133
MA0107.10.688
MA0108.20.0461
MA0111.10.473
MA0112.20.735
MA0113.10.566
MA0114.10.932
MA0115.10.00853
MA0116.10.269
MA0117.10.695
MA0119.17.02101e-4
MA0122.10.623
MA0124.10.437
MA0125.10.158
MA0131.10.0847
MA0135.10.258
MA0136.10.0392
MA0137.20.0107
MA0138.20.0234
MA0139.10.185
MA0140.10.0402
MA0141.10.655
MA0142.10.993
MA0143.10.533
MA0144.10.314
MA0145.10.696
MA0146.10.0237
MA0147.10.0118
MA0148.10.0125
MA0149.10.0295
MA0150.10.222
MA0152.10.0123
MA0153.19.32528e-6
MA0154.10.152
MA0155.10.357
MA0156.10.0163
MA0157.10.175
MA0159.10.289
MA0160.10.101
MA0162.10.887
MA0163.10.759
MA0164.10.0574
MA0258.10.966
MA0259.10.0324



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13526

Novel motifP-value
10.563
100.644
1000.353
1010.0931
1020.156
1030.736
1040.787
1050.36
1060.232
1070.0917
1080.666
1090.576
110.849
1100.9
1110.14
1120.647
1130.614
1140.409
1150.434
1160.811
1174.39016e-4
1180.332
1190.577
120.446
1200.792
1210.414
1220.489
1230.00278
1240.0931
1250.847
1260.287
1270.48
1280.176
1290.823
130.0296
1300.248
1310.0158
1320.171
1330.174
1340.185
1350.0209
1360.016
1370.523
1380.685
1390.278
140.465
1400.102
1410.907
1420.606
1430.562
1440.573
1450.36
1460.605
1470.97
1480.0134
1490.00984
150.466
1500.649
1510.0864
1520.0823
1530.663
1540.943
1550.0256
1560.0555
1570.765
1580.281
1590.948
1600.552
1610.246
1620.209
1630.183
1640.0247
1650.424
1660.00385
1670.662
1680.271
1690.868
170.877
180.384
190.282
20.0787
200.00709
210.472
220.952
230.109
240.338
250.922
260.326
270.0554
280.775
290.00391
30.948
300.538
310.362
320.024
330.465
340.614
350.379
360.582
370.64
380.776
390.484
40.0636
400.391
410.18
420.852
430.371
440.181
450.541
460.849
470.765
480.724
490.43
50.345
500.903
510.568
520.274
530.0409
540.692
550.186
560.491
570.891
580.784
590.334
60.662
600.528
610.11
620.916
630.245
640.521
650.458
660.504
670.328
680.222
690.137
70.983
700.86
710.942
720.762
730.0437
740.248
750.167
760.0215
770.653
780.524
790.87
80.706
800.229
810.132
820.313
830.701
840.328
850.314
860.85
870.0604
880.0465
890.81
90.378
900.996
910.166
920.356
930.133
940.548
950.0839
960.914
970.902
980.0721
990.0809



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13526


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0000349 (extraembryonic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0000351 (trophoblast cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0001062 (anatomical entity)
0000358 (blastocyst)
0000307 (blastula)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000380 (0 days sample)
0000383 (3 days sample)
0000626 (trophoblast cell line sample)
0000643 (mouse trophoblast stem cell line R1AB sample)
0011275 (mouse trophoblast stem cell line B1 differentiation- day00 sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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