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FF:11648-122E1

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Name:Mouse Neurons - ventral spinal cord, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12113
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
tissuespinal cord
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMSC1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005498
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12113 CAGE DRX008851 DRR009723
Accession ID Mm9

Library idBAMCTSS
CNhs12113 DRZ001148 DRZ002533
Accession ID Mm10

Library idBAMCTSS
CNhs12113 DRZ012498 DRZ013883
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

CNhs12113

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.457
10 0
100 0.286
1000 0
1001 --0.0668
1002 0.0198
1003 0.0753
1004 0.0371
1005 --0.0257
1006 0.422
1007 --0.0517
1008 0
1009 --0.2
101 --0.0956
1010 0
1011 0.26
1012 0
1013 --0.0423
1014 0.0508
1015 0.3
1016 0.253
1017 0
1018 0
1019 0
102 0
1020 0.463
1021 0.0742
1022 --0.0498
1023 0
1024 --0.14
1025 0
1026 0
1027 0.278
1028 0
1029 --0.0452
103 --0.0405
1030 0
1031 --0.224
1032 --0.0389
1033 --0.0665
1034 0
1035 0.0742
1036 --0.139
1037 0
1038 0.106
1039 --0.179
104 0
1040 --0.245
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: CNhs12113

Jaspar motif P-value
MA0002.2 2.66653e-4
MA0003.1 0.189
MA0004.1 0.703
MA0006.1 0.144
MA0007.1 0.13
MA0009.1 0.919
MA0014.1 0.55
MA0017.1 1.68141e-5
MA0018.2 0.0213
MA0019.1 0.558
MA0024.1 0.688
MA0025.1 0.472
MA0027.1 0.801
MA0028.1 0.37
MA0029.1 0.799
MA0030.1 0.428
MA0031.1 0.0431
MA0035.2 0.0397
MA0038.1 0.23
MA0039.2 0.0618
MA0040.1 0.588
MA0041.1 0.173
MA0042.1 0.465
MA0043.1 0.146
MA0046.1 1.37939e-8
MA0047.2 5.44481e-5
MA0048.1 0.316
MA0050.1 2.81428e-7
MA0051.1 1.86522e-4
MA0052.1 0.0522
MA0055.1 0.328
MA0057.1 0.169
MA0058.1 0.754
MA0059.1 0.338
MA0060.1 0.00464
MA0061.1 0.0555
MA0062.2 0.0726
MA0065.2 1.01454e-5
MA0066.1 0.0518
MA0067.1 0.571
MA0068.1 0.459
MA0069.1 0.0477
MA0070.1 0.0462
MA0071.1 0.123
MA0072.1 0.09
MA0073.1 0.967
MA0074.1 0.364
MA0076.1 0.855
MA0077.1 0.0437
MA0078.1 0.431
MA0079.2 0.411
MA0080.2 1.36865e-10
MA0081.1 0.483
MA0083.1 0.0584
MA0084.1 0.513
MA0087.1 0.473
MA0088.1 0.189
MA0090.1 0.0607
MA0091.1 0.154
MA0092.1 0.158
MA0093.1 0.756
MA0099.2 1.82694e-4
MA0100.1 0.551
MA0101.1 0.0648
MA0102.2 0.926
MA0103.1 0.0984
MA0104.2 0.849
MA0105.1 0.0221
MA0106.1 0.072
MA0107.1 0.0563
MA0108.2 0.198
MA0111.1 0.9
MA0112.2 6.51549e-5
MA0113.1 0.156
MA0114.1 7.49936e-5
MA0115.1 0.00195
MA0116.1 0.0544
MA0117.1 0.749
MA0119.1 0.0934
MA0122.1 0.728
MA0124.1 0.951
MA0125.1 0.178
MA0131.1 0.832
MA0135.1 0.182
MA0136.1 2.352e-9
MA0137.2 0.141
MA0138.2 0.123
MA0139.1 0.271
MA0140.1 0.00236
MA0141.1 0.00693
MA0142.1 0.121
MA0143.1 0.203
MA0144.1 0.0498
MA0145.1 0.0516
MA0146.1 0.0239
MA0147.1 0.992
MA0148.1 7.62196e-6
MA0149.1 0.0915
MA0150.1 0.0402
MA0152.1 0.0749
MA0153.1 5.15142e-8
MA0154.1 0.0155
MA0155.1 0.51
MA0156.1 1.47699e-5
MA0157.1 0.0246
MA0159.1 0.00412
MA0160.1 0.0458
MA0162.1 0.264
MA0163.1 0.00138
MA0164.1 0.995
MA0258.1 0.00462
MA0259.1 0.779



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: CNhs12113

Novel motif P-value
1 0.124
10 0.0723
100 0.755
101 0.836
102 0.806
103 0.0956
104 0.747
105 0.249
106 0.0157
107 0.0835
108 0.483
109 0.00561
11 0.0695
110 0.0722
111 0.0562
112 0.0038
113 0.898
114 0.206
115 0.606
116 0.493
117 0.0229
118 0.276
119 0.0891
12 0.829
120 0.727
121 0.336
122 0.697
123 0.156
124 0.653
125 0.456
126 0.233
127 0.1
128 0.0388
129 0.134
13 4.26538e-5
130 0.321
131 0.506
132 0.971
133 0.672
134 0.402
135 0.935
136 0.168
137 0.499
138 0.992
139 0.132
14 0.576
140 0.0838
141 0.208
142 0.142
143 0.367
144 0.935
145 0.0107
146 0.418
147 0.781
148 0.447
149 0.195
15 0.0866
150 0.141
151 0.413
152 0.0803
153 0.541
154 0.771
155 0.729
156 9.41785e-4
157 0.279
158 0.0926
159 0.0562
160 0.204
161 0.228
162 0.782
163 0.302
164 0.0257
165 0.0276
166 0.745
167 0.903
168 0.587
169 0.00225
17 0.024
18 0.976
19 0.0709
2 0.842
20 0.292
21 0.408
22 0.0945
23 0.25
24 0.0312
25 0.658
26 3.31154e-5
27 0.884
28 0.451
29 0.0898
3 0.0667
30 0.839
31 0.909
32 0.475
33 0.206
34 0.646
35 0.945
36 0.354
37 0.0196
38 0.318
39 0.229
4 0.569
40 0.302
41 0.553
42 0.163
43 0.117
44 0.639
45 0.581
46 0.0654
47 0.185
48 0.096
49 0.126
5 0.0977
50 0.321
51 0.6
52 0.22
53 0.809
54 0.707
55 0.862
56 0.337
57 0.543
58 0.219
59 0.0762
6 0.722
60 0.0211
61 0.115
62 0.0924
63 0.108
64 0.723
65 0.194
66 0.931
67 0.577
68 0.484
69 0.477
7 0.0256
70 0.0095
71 0.0131
72 0.383
73 0.0289
74 0.251
75 0.0775
76 0.616
77 0.257
78 0.0311
79 0.942
8 0.0809
80 0.809
81 0.672
82 0.208
83 0.282
84 0.749
85 0.0556
86 0.238
87 0.313
88 0.225
89 0.225
9 0.335
90 0.0759
91 0.293
92 0.357
93 0.0232
94 0.7
95 0.0519
96 0.321
97 0.87
98 0.595
99 0.335



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: CNhs12113


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)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002612 (neuron of the ventral spinal cord)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002240 (spinal cord)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002257 (ventral horn of spinal cord)
0001016 (nervous system)
0001137 (dorsum)
0002315 (gray matter of spinal cord)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000207 (mouse neuron of the ventral spinal cord 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:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)