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FF:13297-142H3

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Name:trophoblast stem cell line B1 differentiation
Species:Mouse (Mus musculus)
Library ID:CNhs13526
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
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

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 sample
Ranked 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 sample
Ranked 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

CNhs13526

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -0.0356
1002 -0.102
1003 -0.175
1004 0
1005 -0.294
1006 -0.147
1007 -0.115
1008 0
1009 -0.161
101 0.333
1010 0
1011 -0.178
1012 0
1013 -0.153
1014 -0.0874
1015 -0.132
1016 -0.292
1017 0
1018 0.736
1019 0
102 0
1020 0.222
1021 0.111
1022 -0.0704
1023 0
1024 -0.14
1025 0
1026 0
1027 -0.048
1028 0
1029 -0.115
103 -0.0861
1030 0
1031 -0.508
1032 -0.293
1033 0
1034 0
1035 0
1036 0.105
1037 0
1038 -0.112
1039 -0.189
104 0
1040 -0.0865
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs13526
Jaspar motif P-value
MA0002.2 0.253
MA0003.1 0.663
MA0004.1 0.126
MA0006.1 0.987
MA0007.1 0.861
MA0009.1 0.34
MA0014.1 0.0931
MA0017.1 0.981
MA0018.2 0.00345
MA0019.1 0.679
MA0024.1 1.00463e-4
MA0025.1 0.7
MA0027.1 0.789
MA0028.1 7.57934e-7
MA0029.1 0.00397
MA0030.1 0.659
MA0031.1 0.3
MA0035.2 0.391
MA0038.1 0.635
MA0039.2 8.12767e-6
MA0040.1 0.755
MA0041.1 0.163
MA0042.1 0.43
MA0043.1 0.00229
MA0046.1 3.94587e-11
MA0047.2 0.0219
MA0048.1 0.0303
MA0050.1 0.0386
MA0051.1 0.809
MA0052.1 1.28317e-4
MA0055.1 1.04279e-5
MA0057.1 0.978
MA0058.1 0.0616
MA0059.1 0.0185
MA0060.1 3.00502e-5
MA0061.1 0.54
MA0062.2 2.96043e-9
MA0065.2 0.288
MA0066.1 0.942
MA0067.1 0.306
MA0068.1 0.00324
MA0069.1 0.551
MA0070.1 0.402
MA0071.1 0.053
MA0072.1 0.495
MA0073.1 0.609
MA0074.1 0.775
MA0076.1 4.17421e-6
MA0077.1 0.369
MA0078.1 0.176
MA0079.2 0.193
MA0080.2 0.198
MA0081.1 0.796
MA0083.1 2.47107e-5
MA0084.1 0.616
MA0087.1 0.606
MA0088.1 0.161
MA0090.1 0.3
MA0091.1 0.953
MA0092.1 0.33
MA0093.1 0.118
MA0099.2 5.37098e-8
MA0100.1 0.0253
MA0101.1 0.154
MA0102.2 0.835
MA0103.1 0.0555
MA0104.2 0.0212
MA0105.1 0.172
MA0106.1 0.0133
MA0107.1 0.688
MA0108.2 0.0461
MA0111.1 0.473
MA0112.2 0.735
MA0113.1 0.566
MA0114.1 0.932
MA0115.1 0.00853
MA0116.1 0.269
MA0117.1 0.695
MA0119.1 7.02101e-4
MA0122.1 0.623
MA0124.1 0.437
MA0125.1 0.158
MA0131.1 0.0847
MA0135.1 0.258
MA0136.1 0.0392
MA0137.2 0.0107
MA0138.2 0.0234
MA0139.1 0.185
MA0140.1 0.0402
MA0141.1 0.655
MA0142.1 0.993
MA0143.1 0.533
MA0144.1 0.314
MA0145.1 0.696
MA0146.1 0.0237
MA0147.1 0.0118
MA0148.1 0.0125
MA0149.1 0.0295
MA0150.1 0.222
MA0152.1 0.0123
MA0153.1 9.32528e-6
MA0154.1 0.152
MA0155.1 0.357
MA0156.1 0.0163
MA0157.1 0.175
MA0159.1 0.289
MA0160.1 0.101
MA0162.1 0.887
MA0163.1 0.759
MA0164.1 0.0574
MA0258.1 0.966
MA0259.1 0.0324



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs13526
Novel motif P-value
1 0.563
10 0.644
100 0.353
101 0.0931
102 0.156
103 0.736
104 0.787
105 0.36
106 0.232
107 0.0917
108 0.666
109 0.576
11 0.849
110 0.9
111 0.14
112 0.647
113 0.614
114 0.409
115 0.434
116 0.811
117 4.39016e-4
118 0.332
119 0.577
12 0.446
120 0.792
121 0.414
122 0.489
123 0.00278
124 0.0931
125 0.847
126 0.287
127 0.48
128 0.176
129 0.823
13 0.0296
130 0.248
131 0.0158
132 0.171
133 0.174
134 0.185
135 0.0209
136 0.016
137 0.523
138 0.685
139 0.278
14 0.465
140 0.102
141 0.907
142 0.606
143 0.562
144 0.573
145 0.36
146 0.605
147 0.97
148 0.0134
149 0.00984
15 0.466
150 0.649
151 0.0864
152 0.0823
153 0.663
154 0.943
155 0.0256
156 0.0555
157 0.765
158 0.281
159 0.948
160 0.552
161 0.246
162 0.209
163 0.183
164 0.0247
165 0.424
166 0.00385
167 0.662
168 0.271
169 0.868
17 0.877
18 0.384
19 0.282
2 0.0787
20 0.00709
21 0.472
22 0.952
23 0.109
24 0.338
25 0.922
26 0.326
27 0.0554
28 0.775
29 0.00391
3 0.948
30 0.538
31 0.362
32 0.024
33 0.465
34 0.614
35 0.379
36 0.582
37 0.64
38 0.776
39 0.484
4 0.0636
40 0.391
41 0.18
42 0.852
43 0.371
44 0.181
45 0.541
46 0.849
47 0.765
48 0.724
49 0.43
5 0.345
50 0.903
51 0.568
52 0.274
53 0.0409
54 0.692
55 0.186
56 0.491
57 0.891
58 0.784
59 0.334
6 0.662
60 0.528
61 0.11
62 0.916
63 0.245
64 0.521
65 0.458
66 0.504
67 0.328
68 0.222
69 0.137
7 0.983
70 0.86
71 0.942
72 0.762
73 0.0437
74 0.248
75 0.167
76 0.0215
77 0.653
78 0.524
79 0.87
8 0.706
80 0.229
81 0.132
82 0.313
83 0.701
84 0.328
85 0.314
86 0.85
87 0.0604
88 0.0465
89 0.81
9 0.378
90 0.996
91 0.166
92 0.356
93 0.133
94 0.548
95 0.0839
96 0.914
97 0.902
98 0.0721
99 0.0809



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

library id: CNhs13526


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)
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)
Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship

Analyst: Hideya Kawaji

link to source data

data


NA