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FF:11640-122D2

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Name:Mouse Mesenchymal stem cells - bone marrow derived, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12616
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMCS3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004986
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12616 CAGE DRX008827 DRR009699
Accession ID Mm9

Library idBAMCTSS
CNhs12616 DRZ001124 DRZ002509
Accession ID Mm10

Library idBAMCTSS
CNhs12616 DRZ012474 DRZ013859
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

CNhs12616

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0668
1002 --0.0156
1003 --0.0349
1004 0
1005 0
1006 0.212
1007 --0.426
1008 0
1009 --0.19
101 --0.54
1010 0
1011 0
1012 0
1013 0.0678
1014 --0.0874
1015 0.00844
1016 --0.232
1017 0
1018 0
1019 0
102 0
1020 0.658
1021 0.23
1022 --0.0446
1023 0
1024 --0.14
1025 --0.0611
1026 0
1027 0
1028 0
1029 --0.176
103 0
1030 0
1031 --0.243
1032 --0.184
1033 --0.0752
1034 0
1035 0
1036 --0.185
1037 0
1038 --0.14
1039 --0.11
104 0
1040 --0.0211
1041 0.233



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: CNhs12616

Jaspar motif P-value
MA0002.2 5.06249e-6
MA0003.1 0.133
MA0004.1 0.414
MA0006.1 0.504
MA0007.1 0.628
MA0009.1 0.76
MA0014.1 0.698
MA0017.1 0.105
MA0018.2 0.12
MA0019.1 0.743
MA0024.1 0.00543
MA0025.1 0.483
MA0027.1 0.512
MA0028.1 0.573
MA0029.1 0.951
MA0030.1 0.211
MA0031.1 0.698
MA0035.2 0.382
MA0038.1 1.77467e-4
MA0039.2 0.782
MA0040.1 0.769
MA0041.1 0.479
MA0042.1 0.799
MA0043.1 0.146
MA0046.1 1.01955e-4
MA0047.2 0.723
MA0048.1 0.677
MA0050.1 3.89121e-6
MA0051.1 5.8423e-4
MA0052.1 0.0399
MA0055.1 0.987
MA0057.1 0.28
MA0058.1 0.26
MA0059.1 0.244
MA0060.1 7.57707e-13
MA0061.1 0.0303
MA0062.2 0.28
MA0065.2 0.00357
MA0066.1 0.0315
MA0067.1 0.698
MA0068.1 0.636
MA0069.1 0.741
MA0070.1 0.198
MA0071.1 0.138
MA0072.1 0.407
MA0073.1 0.592
MA0074.1 0.0174
MA0076.1 0.255
MA0077.1 0.516
MA0078.1 0.539
MA0079.2 0.566
MA0080.2 3.02804e-13
MA0081.1 0.00289
MA0083.1 0.405
MA0084.1 0.98
MA0087.1 0.527
MA0088.1 0.379
MA0090.1 0.8
MA0091.1 0.253
MA0092.1 0.394
MA0093.1 0.435
MA0099.2 4.10203e-4
MA0100.1 0.859
MA0101.1 0.141
MA0102.2 0.754
MA0103.1 0.706
MA0104.2 0.833
MA0105.1 0.00555
MA0106.1 0.22
MA0107.1 0.144
MA0108.2 0.181
MA0111.1 0.313
MA0112.2 9.40663e-5
MA0113.1 0.267
MA0114.1 0.251
MA0115.1 0.814
MA0116.1 0.00187
MA0117.1 0.875
MA0119.1 0.217
MA0122.1 0.502
MA0124.1 0.764
MA0125.1 0.074
MA0131.1 0.155
MA0135.1 0.681
MA0136.1 2.23736e-10
MA0137.2 0.738
MA0138.2 0.458
MA0139.1 0.108
MA0140.1 0.274
MA0141.1 0.0126
MA0142.1 0.816
MA0143.1 0.214
MA0144.1 0.415
MA0145.1 0.0506
MA0146.1 0.00606
MA0147.1 0.777
MA0148.1 0.641
MA0149.1 0.213
MA0150.1 0.0114
MA0152.1 0.245
MA0153.1 0.00269
MA0154.1 0.00452
MA0155.1 0.395
MA0156.1 0.00297
MA0157.1 0.667
MA0159.1 0.00298
MA0160.1 0.142
MA0162.1 0.202
MA0163.1 3.81235e-5
MA0164.1 0.959
MA0258.1 0.00667
MA0259.1 0.584



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: CNhs12616

Novel motif P-value
1 0.126
10 0.0691
100 0.808
101 0.968
102 0.429
103 0.118
104 0.799
105 0.552
106 0.0215
107 0.285
108 0.393
109 0.0227
11 0.0569
110 0.085
111 0.0483
112 0.0938
113 0.751
114 0.0259
115 0.435
116 0.104
117 0.0546
118 0.421
119 0.234
12 0.814
120 0.0635
121 0.453
122 0.833
123 0.607
124 0.931
125 0.277
126 0.378
127 0.241
128 0.0377
129 0.0984
13 0.11
130 0.615
131 0.108
132 0.402
133 0.131
134 0.684
135 0.855
136 0.696
137 0.49
138 0.462
139 0.284
14 0.48
140 0.233
141 0.254
142 0.217
143 0.0216
144 0.93
145 0.173
146 0.624
147 0.85
148 0.0789
149 0.0144
15 0.103
150 0.147
151 0.206
152 0.0899
153 0.79
154 0.603
155 0.408
156 0.46
157 0.567
158 0.552
159 0.846
160 0.468
161 0.0728
162 0.783
163 0.831
164 0.182
165 0.177
166 0.673
167 0.409
168 0.517
169 0.00641
17 0.0221
18 0.0909
19 0.159
2 0.522
20 0.36
21 0.336
22 0.11
23 0.116
24 0.106
25 0.762
26 0.0117
27 0.49
28 0.756
29 0.0694
3 0.0267
30 0.744
31 0.244
32 0.166
33 0.331
34 0.362
35 0.573
36 0.013
37 0.0397
38 0.192
39 0.689
4 0.31
40 0.0653
41 0.36
42 0.225
43 0.0486
44 0.0411
45 0.516
46 0.066
47 0.234
48 0.188
49 0.0743
5 0.253
50 0.483
51 0.805
52 0.467
53 0.978
54 0.737
55 0.581
56 0.196
57 0.418
58 0.387
59 0.0071
6 0.885
60 0.123
61 0.444
62 0.136
63 0.11
64 0.243
65 0.0355
66 0.728
67 0.158
68 0.00837
69 0.119
7 0.427
70 6.16872e-4
71 0.035
72 0.151
73 0.0357
74 0.725
75 0.0551
76 0.462
77 0.118
78 0.0475
79 0.651
8 0.0486
80 0.991
81 0.15
82 0.244
83 0.714
84 0.391
85 0.0771
86 0.449
87 0.209
88 0.9
89 0.0915
9 0.547
90 0.306
91 0.235
92 0.0871
93 0.418
94 0.496
95 0.048
96 0.567
97 0.839
98 0.0499
99 0.93



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: CNhs12616


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002092 (bone marrow cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000112 (mouse mesenchymal stem cell of bone marrow 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

CL:0000134 (mesenchymal cell)