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FF:11736-123E8

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Name:Mouse Microglia, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12634
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
tissuebrain
dev stageNA
sexNA
ageNA
cell typemicroglial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMG2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005410
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12634 CAGE DRX008829 DRR009701
Accession ID Mm9

Library idBAMCTSS
CNhs12634 DRZ001126 DRZ002511
Accession ID Mm10

Library idBAMCTSS
CNhs12634 DRZ012476 DRZ013861
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

CNhs12634

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.664
1001 -0.0749
1002 0.0639
1003 0.583
1004 0
1005 0
1006 0.256
1007 -0.229
1008 0
1009 0.0576
101 -0.552
1010 0
1011 0.0337
1012 0
1013 0.117
1014 0
1015 0.256
1016 0.213
1017 0
1018 0
1019 0
102 0
1020 0.61
1021 0.141
1022 0.012
1023 0
1024 -0.156
1025 -0.0196
1026 0
1027 0.405
1028 0.141
1029 -0.176
103 0.164
1030 0
1031 0.403
1032 0.756
1033 -0.0665
1034 0
1035 0
1036 -0.183
1037 0
1038 -0.217
1039 0.127
104 0
1040 0.283
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: CNhs12634
Jaspar motif P-value
MA0002.2 0.621
MA0003.1 0.153
MA0004.1 0.383
MA0006.1 0.405
MA0007.1 0.61
MA0009.1 0.159
MA0014.1 0.787
MA0017.1 9.73702e-4
MA0018.2 0.586
MA0019.1 0.23
MA0024.1 0.00289
MA0025.1 0.837
MA0027.1 0.245
MA0028.1 5.23907e-4
MA0029.1 0.656
MA0030.1 0.677
MA0031.1 0.601
MA0035.2 0.00184
MA0038.1 0.0678
MA0039.2 0.928
MA0040.1 0.47
MA0041.1 0.258
MA0042.1 0.726
MA0043.1 0.936
MA0046.1 2.79439e-6
MA0047.2 0.106
MA0048.1 0.443
MA0050.1 0.34
MA0051.1 0.81
MA0052.1 0.34
MA0055.1 0.652
MA0057.1 0.682
MA0058.1 0.589
MA0059.1 0.946
MA0060.1 0.985
MA0061.1 0.601
MA0062.2 3.25868e-6
MA0065.2 0.833
MA0066.1 0.616
MA0067.1 0.185
MA0068.1 0.598
MA0069.1 0.211
MA0070.1 0.368
MA0071.1 0.301
MA0072.1 0.321
MA0073.1 0.921
MA0074.1 0.227
MA0076.1 0.00129
MA0077.1 0.372
MA0078.1 0.548
MA0079.2 0.0146
MA0080.2 0.0695
MA0081.1 0.754
MA0083.1 0.975
MA0084.1 0.374
MA0087.1 0.955
MA0088.1 0.552
MA0090.1 0.914
MA0091.1 0.307
MA0092.1 0.805
MA0093.1 0.438
MA0099.2 0.675
MA0100.1 0.627
MA0101.1 0.332
MA0102.2 0.214
MA0103.1 0.123
MA0104.2 0.429
MA0105.1 0.815
MA0106.1 0.424
MA0107.1 0.413
MA0108.2 0.367
MA0111.1 0.529
MA0112.2 0.751
MA0113.1 0.864
MA0114.1 0.00386
MA0115.1 0.0212
MA0116.1 0.709
MA0117.1 0.539
MA0119.1 0.616
MA0122.1 0.872
MA0124.1 0.778
MA0125.1 0.637
MA0131.1 0.0957
MA0135.1 0.0752
MA0136.1 0.0266
MA0137.2 0.428
MA0138.2 0.58
MA0139.1 0.642
MA0140.1 3.80558e-5
MA0141.1 0.814
MA0142.1 0.8
MA0143.1 0.827
MA0144.1 0.203
MA0145.1 0.136
MA0146.1 0.0408
MA0147.1 0.473
MA0148.1 0.0258
MA0149.1 0.191
MA0150.1 0.23
MA0152.1 0.076
MA0153.1 4.93809e-4
MA0154.1 0.205
MA0155.1 0.085
MA0156.1 6.7189e-5
MA0157.1 0.478
MA0159.1 0.776
MA0160.1 0.141
MA0162.1 0.351
MA0163.1 0.114
MA0164.1 0.823
MA0258.1 0.975
MA0259.1 0.132



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: CNhs12634
Novel motif P-value
1 0.318
10 0.471
100 0.996
101 0.984
102 0.75
103 0.222
104 0.94
105 0.893
106 0.098
107 0.947
108 0.29
109 0.266
11 0.814
110 0.738
111 0.594
112 0.407
113 0.411
114 0.88
115 0.801
116 0.126
117 0.14
118 0.675
119 0.126
12 0.917
120 0.316
121 0.591
122 0.567
123 0.728
124 0.952
125 0.114
126 0.42
127 0.97
128 0.592
129 0.119
13 0.101
130 0.837
131 0.771
132 0.109
133 0.826
134 0.744
135 0.103
136 0.0506
137 0.423
138 0.525
139 0.039
14 0.326
140 0.0583
141 0.257
142 0.0231
143 0.855
144 0.837
145 0.118
146 0.631
147 0.94
148 0.861
149 0.148
15 0.205
150 0.307
151 0.312
152 0.0404
153 0.13
154 0.0611
155 0.816
156 0.0164
157 0.335
158 0.0168
159 0.218
160 0.622
161 0.559
162 0.584
163 0.152
164 3.20609e-4
165 0.992
166 0.981
167 0.0431
168 0.605
169 0.268
17 0.653
18 0.804
19 0.619
2 0.0258
20 0.76
21 0.44
22 0.175
23 0.129
24 0.592
25 0.167
26 0.729
27 0.528
28 0.314
29 0.127
3 0.696
30 0.105
31 0.315
32 0.00711
33 0.7
34 0.0296
35 0.492
36 0.55
37 0.576
38 0.55
39 0.434
4 0.862
40 0.544
41 0.815
42 0.665
43 0.51
44 0.313
45 0.179
46 0.41
47 0.872
48 0.918
49 0.366
5 0.0567
50 0.179
51 0.777
52 0.0736
53 0.762
54 0.635
55 0.366
56 0.391
57 0.549
58 0.182
59 0.00895
6 0.993
60 0.371
61 0.418
62 0.398
63 0.174
64 0.762
65 0.0785
66 0.626
67 0.663
68 0.254
69 0.0994
7 0.0476
70 0.984
71 0.593
72 0.785
73 0.0762
74 0.348
75 0.64
76 0.116
77 0.00817
78 0.00452
79 0.865
8 0.596
80 0.547
81 0.369
82 0.421
83 0.481
84 0.417
85 0.468
86 0.86
87 0.00126
88 0.266
89 0.685
9 0.735
90 0.191
91 0.815
92 0.396
93 0.0887
94 0.0157
95 0.197
96 0.11
97 0.895
98 0.2
99 0.204



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: CNhs12634


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000878 (central nervous system macrophage)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000125 (glial cell)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)
0000864 (tissue-resident macrophage)
0000129 (microglial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000113 (mouse microglial cell 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)