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FF:13283-142F7

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Name:trophoblast stem cell line R1AB differentiation
Species:Mouse (Mus musculus)
Library ID:CNhs13481
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationHirohiko Kodeki(RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberR1AB +d0
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005466
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13481 CAGE DRX008917 DRR009791
Accession ID Mm9

Library idBAMCTSS
CNhs13481 DRZ001216 DRZ002599
Accession ID Mm10

Library idBAMCTSS
CNhs13481 DRZ012566 DRZ013949
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.
Analyst:NA

link to dataset.
data

CNhs13481

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.0975
1003 --0.156
1004 0.0717
1005 --0.429
1006 --0.143
1007 --0.0573
1008 0
1009 --0.188
101 0.457
1010 0
1011 --0.0801
1012 0
1013 --0.145
1014 --0.0874
1015 --0.00286
1016 --0.328
1017 0
1018 0.588
1019 0
102 0
1020 0.0717
1021 0.0717
1022 0
1023 0
1024 --0.14
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.0775
103 --0.0848
1030 0
1031 --0.536
1032 --0.583
1033 0.143
1034 0
1035 0
1036 0.28
1037 0
1038 --0.123
1039 --0.344
104 0
1040 --0.0865
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



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


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13481

Jaspar motif P-value
MA0002.2 0.125
MA0003.1 0.861
MA0004.1 0.0967
MA0006.1 0.989
MA0007.1 0.977
MA0009.1 0.285
MA0014.1 0.41
MA0017.1 0.674
MA0018.2 0.0412
MA0019.1 0.483
MA0024.1 7.36205e-4
MA0025.1 0.141
MA0027.1 0.866
MA0028.1 4.95951e-9
MA0029.1 0.0281
MA0030.1 0.0455
MA0031.1 0.00799
MA0035.2 0.126
MA0038.1 0.511
MA0039.2 3.11489e-4
MA0040.1 0.485
MA0041.1 0.355
MA0042.1 0.875
MA0043.1 0.0262
MA0046.1 2.33362e-15
MA0047.2 1.29614e-4
MA0048.1 0.00571
MA0050.1 4.10606e-5
MA0051.1 0.0285
MA0052.1 6.12687e-6
MA0055.1 2.34921e-5
MA0057.1 0.955
MA0058.1 0.0431
MA0059.1 0.00385
MA0060.1 0.023
MA0061.1 0.76
MA0062.2 4.06262e-12
MA0065.2 0.225
MA0066.1 0.867
MA0067.1 0.506
MA0068.1 0.0526
MA0069.1 0.75
MA0070.1 0.329
MA0071.1 0.0589
MA0072.1 0.571
MA0073.1 0.682
MA0074.1 0.36
MA0076.1 7.43519e-9
MA0077.1 0.782
MA0078.1 0.274
MA0079.2 0.872
MA0080.2 0.424
MA0081.1 0.529
MA0083.1 0.00537
MA0084.1 0.14
MA0087.1 0.744
MA0088.1 0.344
MA0090.1 0.889
MA0091.1 0.899
MA0092.1 0.172
MA0093.1 0.102
MA0099.2 3.52375e-5
MA0100.1 0.0172
MA0101.1 0.23
MA0102.2 0.628
MA0103.1 0.467
MA0104.2 0.0346
MA0105.1 0.884
MA0106.1 0.0134
MA0107.1 0.824
MA0108.2 0.00281
MA0111.1 0.521
MA0112.2 0.835
MA0113.1 0.723
MA0114.1 0.882
MA0115.1 0.00389
MA0116.1 0.962
MA0117.1 0.881
MA0119.1 0.00762
MA0122.1 0.544
MA0124.1 0.484
MA0125.1 0.202
MA0131.1 0.0845
MA0135.1 0.172
MA0136.1 0.00225
MA0137.2 0.0669
MA0138.2 0.0021
MA0139.1 0.465
MA0140.1 0.0205
MA0141.1 0.308
MA0142.1 0.811
MA0143.1 0.646
MA0144.1 0.383
MA0145.1 0.516
MA0146.1 0.0548
MA0147.1 0.0114
MA0148.1 4.25595e-4
MA0149.1 0.0459
MA0150.1 0.212
MA0152.1 0.404
MA0153.1 2.15586e-7
MA0154.1 0.385
MA0155.1 0.568
MA0156.1 3.64395e-4
MA0157.1 0.00555
MA0159.1 0.339
MA0160.1 0.099
MA0162.1 0.615
MA0163.1 0.214
MA0164.1 0.0223
MA0258.1 0.511
MA0259.1 0.0369



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13481

Novel motif P-value
1 0.673
10 0.224
100 0.233
101 0.0711
102 0.14
103 0.713
104 0.717
105 0.324
106 0.239
107 0.0738
108 0.503
109 0.328
11 0.715
110 0.597
111 0.0892
112 0.878
113 0.298
114 0.803
115 0.363
116 0.512
117 5.62093e-4
118 0.34
119 0.372
12 0.613
120 0.478
121 0.923
122 0.254
123 0.0306
124 0.0236
125 0.316
126 0.395
127 0.279
128 0.187
129 0.912
13 0.0109
130 0.157
131 0.0157
132 0.241
133 0.0467
134 0.192
135 0.0215
136 0.0563
137 0.61
138 0.8
139 0.532
14 0.392
140 0.13
141 0.61
142 0.554
143 0.322
144 0.575
145 0.301
146 0.429
147 0.853
148 0.122
149 0.00528
15 0.632
150 0.665
151 0.136
152 0.122
153 0.75
154 0.699
155 0.0565
156 0.419
157 0.9
158 0.436
159 0.678
160 0.541
161 0.318
162 0.245
163 0.281
164 0.0158
165 0.604
166 0.0272
167 0.987
168 0.0645
169 0.7
17 0.786
18 0.499
19 0.31
2 0.0531
20 0.00389
21 0.238
22 0.814
23 0.0636
24 0.29
25 0.881
26 0.303
27 0.0459
28 0.752
29 0.00555
3 0.753
30 0.366
31 0.292
32 0.0981
33 0.463
34 0.464
35 0.623
36 0.285
37 0.251
38 0.661
39 0.543
4 0.147
40 0.458
41 0.155
42 0.731
43 0.521
44 0.378
45 0.426
46 0.822
47 0.62
48 0.509
49 0.533
5 0.635
50 0.911
51 0.795
52 0.168
53 0.0493
54 0.788
55 0.491
56 0.464
57 0.731
58 0.822
59 0.329
6 0.814
60 0.372
61 0.107
62 0.803
63 0.406
64 0.599
65 0.449
66 0.733
67 0.348
68 0.335
69 0.444
7 0.768
70 0.411
71 0.332
72 0.921
73 0.00652
74 0.334
75 0.0502
76 0.015
77 0.696
78 0.382
79 0.67
8 0.382
80 0.158
81 0.138
82 0.22
83 0.54
84 0.563
85 0.33
86 0.48
87 0.183
88 0.0482
89 0.516
9 0.379
90 0.342
91 0.737
92 0.288
93 0.168
94 0.607
95 0.016
96 0.634
97 0.999
98 0.0645
99 0.262



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs13481


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
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)
0000626 (trophoblast cell line sample)
0000643 (mouse trophoblast stem cell line R1AB sample)
0000644 (trophoblast cell line differentiation sample)
0011194 (mouse trophoblast stem cell line R1AB differentiation- day00 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA