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FF:13290-142G5

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Name:trophoblast stem cell line Rybp differentiation
Species:Mouse (Mus musculus)
Library ID:CNhs13519
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 numberRybp +d0
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004700
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13519 CAGE DRX008918 DRR009792
Accession ID Mm9

Library idBAMCTSS
CNhs13519 DRZ001217 DRZ002600
Accession ID Mm10

Library idBAMCTSS
CNhs13519 DRZ012567 DRZ013950
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

CNhs13519

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00178
1001 --0.0631
1002 --0.0941
1003 --0.175
1004 0
1005 --0.111
1006 --0.248
1007 --0.124
1008 0
1009 --0.19
101 0.318
1010 0
1011 --0.0725
1012 0
1013 --0.115
1014 --0.0874
1015 --0.063
1016 --0.327
1017 0
1018 0.793
1019 0
102 0
1020 0.177
1021 0.077
1022 --0.124
1023 0
1024 --0.14
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0861
1030 0
1031 --0.521
1032 --0.458
1033 0.0595
1034 0
1035 0
1036 --0.0321
1037 0
1038 --0.0973
1039 --0.281
104 0
1040 --0.0535
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: CNhs13519

Jaspar motif P-value
MA0002.2 0.21
MA0003.1 0.738
MA0004.1 0.239
MA0006.1 0.987
MA0007.1 0.869
MA0009.1 0.336
MA0014.1 0.0949
MA0017.1 0.761
MA0018.2 0.00107
MA0019.1 0.525
MA0024.1 0.00164
MA0025.1 0.347
MA0027.1 0.843
MA0028.1 9.22102e-8
MA0029.1 2.56211e-4
MA0030.1 0.268
MA0031.1 0.0398
MA0035.2 0.173
MA0038.1 0.851
MA0039.2 3.27972e-6
MA0040.1 0.904
MA0041.1 0.185
MA0042.1 0.613
MA0043.1 0.00613
MA0046.1 1.78922e-12
MA0047.2 0.00571
MA0048.1 0.0248
MA0050.1 5.59512e-5
MA0051.1 0.0799
MA0052.1 2.43036e-5
MA0055.1 6.18729e-6
MA0057.1 0.525
MA0058.1 0.119
MA0059.1 0.0358
MA0060.1 0.00204
MA0061.1 0.826
MA0062.2 1.13817e-10
MA0065.2 0.31
MA0066.1 0.837
MA0067.1 0.248
MA0068.1 0.00301
MA0069.1 0.857
MA0070.1 0.53
MA0071.1 0.0803
MA0072.1 0.329
MA0073.1 0.575
MA0074.1 0.414
MA0076.1 3.85008e-7
MA0077.1 0.796
MA0078.1 0.235
MA0079.2 0.192
MA0080.2 0.378
MA0081.1 0.862
MA0083.1 0.0261
MA0084.1 0.598
MA0087.1 0.554
MA0088.1 0.155
MA0090.1 0.407
MA0091.1 0.778
MA0092.1 0.541
MA0093.1 0.217
MA0099.2 2.86627e-9
MA0100.1 0.0307
MA0101.1 0.215
MA0102.2 0.759
MA0103.1 0.0804
MA0104.2 0.081
MA0105.1 0.446
MA0106.1 0.00284
MA0107.1 0.688
MA0108.2 0.172
MA0111.1 0.394
MA0112.2 0.745
MA0113.1 0.425
MA0114.1 0.961
MA0115.1 0.00624
MA0116.1 0.654
MA0117.1 0.871
MA0119.1 0.00133
MA0122.1 0.581
MA0124.1 0.382
MA0125.1 0.663
MA0131.1 0.0609
MA0135.1 0.798
MA0136.1 0.0198
MA0137.2 0.0197
MA0138.2 0.00707
MA0139.1 0.273
MA0140.1 0.0237
MA0141.1 0.891
MA0142.1 0.694
MA0143.1 0.835
MA0144.1 0.174
MA0145.1 0.784
MA0146.1 0.00548
MA0147.1 0.0386
MA0148.1 0.00651
MA0149.1 0.0368
MA0150.1 0.231
MA0152.1 0.0555
MA0153.1 4.59169e-6
MA0154.1 0.456
MA0155.1 0.443
MA0156.1 0.0111
MA0157.1 0.049
MA0159.1 0.361
MA0160.1 0.157
MA0162.1 0.691
MA0163.1 0.977
MA0164.1 0.0215
MA0258.1 0.75
MA0259.1 0.043



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: CNhs13519

Novel motif P-value
1 0.418
10 0.409
100 0.427
101 0.0394
102 0.0654
103 0.942
104 0.705
105 0.303
106 0.257
107 0.0809
108 0.826
109 0.453
11 0.913
110 0.845
111 0.0434
112 0.863
113 0.566
114 0.901
115 0.587
116 0.794
117 2.98606e-4
118 0.346
119 0.653
12 0.596
120 0.746
121 0.769
122 0.396
123 0.0115
124 0.0796
125 0.777
126 0.441
127 0.338
128 0.136
129 0.689
13 0.00622
130 0.0677
131 0.00449
132 0.196
133 0.0429
134 0.256
135 0.00932
136 0.019
137 0.565
138 0.54
139 0.706
14 0.396
140 0.316
141 0.91
142 0.729
143 0.294
144 0.697
145 0.585
146 0.533
147 0.923
148 0.0349
149 0.0517
15 0.379
150 0.637
151 0.174
152 0.0503
153 0.909
154 0.855
155 0.0513
156 0.00987
157 0.538
158 0.456
159 0.891
160 0.583
161 0.0905
162 0.32
163 0.192
164 0.0193
165 0.742
166 0.0224
167 0.865
168 0.0764
169 0.34
17 0.957
18 0.422
19 0.478
2 0.161
20 0.00903
21 0.385
22 0.84
23 0.118
24 0.215
25 0.951
26 0.573
27 0.0308
28 0.837
29 0.00671
3 0.746
30 0.495
31 0.238
32 0.0297
33 0.722
34 0.697
35 0.242
36 0.575
37 0.268
38 0.88
39 0.785
4 0.0966
40 0.437
41 0.171
42 0.708
43 0.368
44 0.222
45 0.531
46 0.953
47 0.649
48 0.754
49 0.448
5 0.306
50 0.685
51 0.605
52 0.258
53 0.0572
54 0.816
55 0.335
56 0.589
57 0.752
58 0.966
59 0.278
6 0.611
60 0.573
61 0.136
62 0.881
63 0.339
64 0.389
65 0.533
66 0.534
67 0.3
68 0.358
69 0.265
7 0.802
70 0.369
71 0.696
72 0.88
73 0.0078
74 0.211
75 0.0462
76 0.0256
77 0.766
78 0.242
79 0.851
8 0.663
80 0.308
81 0.224
82 0.424
83 0.722
84 0.376
85 0.455
86 0.553
87 0.0497
88 0.0234
89 0.763
9 0.437
90 0.704
91 0.433
92 0.497
93 0.101
94 0.322
95 0.0128
96 0.845
97 0.908
98 0.0171
99 0.184



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: CNhs13519


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)
0000644 (trophoblast cell line differentiation sample)
0000642 (mouse trophoblast stem cell line Rybp sample)
0011201 (mouse trophoblast stem cell line Rybp 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