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FF:11815-124E6

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Name:CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool1 (C57BL_6J)
Species:Mouse (Mus musculus)
Library ID:CNhs13218
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
strainC57BL/6J
tissueblood
dev stageNA
sexNA
ageNA
cell typeT cell
cell lineNA
companyNA
collaborationMorikawa (University of Kyoto)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB6Ts3/28-6
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005830
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13218 CAGE DRX008793 DRR009665
Accession ID Mm9

Library idBAMCTSS
CNhs13218 DRZ001090 DRZ002475
Accession ID Mm10

Library idBAMCTSS
CNhs13218 DRZ012440 DRZ013825
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

CNhs13218

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.116
1003 --0.087
1004 0
1005 0
1006 --0.436
1007 --0.122
1008 0
1009 --0.2
101 0.71
1010 0
1011 0.153
1012 0
1013 --0.331
1014 --0.0243
1015 0.212
1016 --0.61
1017 0
1018 0
1019 0
102 0.307
1020 0.128
1021 0
1022 --0.223
1023 0
1024 --0.307
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.115
103 --0.0887
1030 0
1031 -1.193
1032 --0.602
1033 0.661
1034 0
1035 0
1036 0.631
1037 0
1038 --0.481
1039 --0.348
104 0
1040 --0.216
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: CNhs13218

Jaspar motif P-value
MA0002.2 0.0067
MA0003.1 0.273
MA0004.1 0.00463
MA0006.1 0.137
MA0007.1 0.346
MA0009.1 0.924
MA0014.1 0.73
MA0017.1 0.244
MA0018.2 0.00188
MA0019.1 0.521
MA0024.1 0.369
MA0025.1 0.71
MA0027.1 0.43
MA0028.1 4.55556e-8
MA0029.1 0.535
MA0030.1 0.246
MA0031.1 0.873
MA0035.2 0.622
MA0038.1 0.00635
MA0039.2 0.0351
MA0040.1 0.278
MA0041.1 0.143
MA0042.1 0.532
MA0043.1 0.0386
MA0046.1 1.16911e-9
MA0047.2 0.844
MA0048.1 0.0996
MA0050.1 0.111
MA0051.1 0.458
MA0052.1 0.0737
MA0055.1 0.00747
MA0057.1 0.707
MA0058.1 0.00283
MA0059.1 6.4326e-7
MA0060.1 1.93449e-10
MA0061.1 5.04248e-5
MA0062.2 1.33131e-17
MA0065.2 0.133
MA0066.1 0.194
MA0067.1 0.0792
MA0068.1 0.218
MA0069.1 0.848
MA0070.1 0.463
MA0071.1 0.134
MA0072.1 0.123
MA0073.1 0.763
MA0074.1 0.259
MA0076.1 1.44856e-9
MA0077.1 0.432
MA0078.1 0.211
MA0079.2 0.0259
MA0080.2 9.31245e-8
MA0081.1 0.00453
MA0083.1 0.428
MA0084.1 0.214
MA0087.1 0.913
MA0088.1 0.354
MA0090.1 0.127
MA0091.1 0.238
MA0092.1 0.667
MA0093.1 0.00678
MA0099.2 0.0132
MA0100.1 0.244
MA0101.1 1.49296e-7
MA0102.2 0.565
MA0103.1 0.229
MA0104.2 5.43602e-6
MA0105.1 4.6811e-6
MA0106.1 0.711
MA0107.1 4.38625e-6
MA0108.2 2.23758e-4
MA0111.1 0.256
MA0112.2 0.067
MA0113.1 0.31
MA0114.1 0.972
MA0115.1 0.0397
MA0116.1 0.0317
MA0117.1 0.344
MA0119.1 0.467
MA0122.1 0.55
MA0124.1 0.987
MA0125.1 0.0709
MA0131.1 0.23
MA0135.1 0.334
MA0136.1 8.7591e-18
MA0137.2 2.4542e-4
MA0138.2 0.0365
MA0139.1 0.471
MA0140.1 0.915
MA0141.1 0.102
MA0142.1 0.291
MA0143.1 0.711
MA0144.1 0.073
MA0145.1 0.213
MA0146.1 0.924
MA0147.1 8.67113e-8
MA0148.1 0.896
MA0149.1 0.0678
MA0150.1 0.0537
MA0152.1 0.227
MA0153.1 1.60579e-4
MA0154.1 0.206
MA0155.1 0.797
MA0156.1 1.00072e-15
MA0157.1 0.72
MA0159.1 0.0913
MA0160.1 0.133
MA0162.1 0.775
MA0163.1 0.00446
MA0164.1 0.157
MA0258.1 0.024
MA0259.1 0.0107



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: CNhs13218

Novel motif P-value
1 0.128
10 0.0433
100 0.527
101 0.608
102 0.386
103 0.429
104 0.477
105 0.525
106 0.521
107 0.687
108 0.821
109 0.147
11 0.135
110 0.026
111 0.00892
112 0.0772
113 0.924
114 0.0657
115 0.841
116 0.704
117 5.12485e-4
118 0.545
119 0.476
12 0.491
120 0.176
121 0.525
122 0.971
123 0.669
124 0.259
125 0.0755
126 0.131
127 0.558
128 0.44
129 0.423
13 0.0637
130 0.541
131 0.454
132 0.686
133 0.067
134 0.438
135 0.749
136 0.249
137 0.621
138 0.328
139 0.00777
14 0.196
140 0.098
141 0.475
142 0.28
143 0.0136
144 0.546
145 0.0301
146 0.857
147 0.792
148 0.252
149 0.491
15 0.157
150 0.768
151 0.703
152 0.214
153 0.177
154 0.419
155 0.321
156 0.0196
157 0.534
158 0.0166
159 0.925
160 0.781
161 0.0543
162 0.391
163 0.938
164 0.0135
165 0.307
166 0.065
167 0.021
168 0.82
169 0.703
17 0.521
18 0.0957
19 0.277
2 0.164
20 0.00557
21 0.124
22 0.772
23 0.49
24 0.517
25 0.192
26 0.0317
27 0.509
28 0.661
29 0.0207
3 0.307
30 0.112
31 0.814
32 0.543
33 0.173
34 0.364
35 0.0741
36 0.045
37 0.175
38 1
39 0.89
4 0.625
40 0.394
41 0.146
42 0.414
43 0.54
44 0.296
45 0.477
46 0.167
47 0.466
48 0.189
49 0.149
5 0.0903
50 0.751
51 0.939
52 0.231
53 0.727
54 0.842
55 0.41
56 0.932
57 0.364
58 0.32
59 0.975
6 0.767
60 0.76
61 0.144
62 0.0844
63 0.588
64 0.529
65 0.775
66 0.357
67 0.568
68 0.0895
69 0.645
7 0.31
70 0.00239
71 0.0106
72 0.451
73 0.251
74 0.811
75 0.0104
76 0.00696
77 0.518
78 0.0329
79 0.6
8 0.0832
80 0.242
81 0.677
82 0.158
83 0.268
84 0.414
85 0.919
86 0.193
87 0.96
88 0.449
89 0.626
9 0.978
90 0.0183
91 0.937
92 0.0735
93 0.158
94 0.208
95 0.182
96 0.0389
97 0.537
98 0.527
99 0.264



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: CNhs13218


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000791 (mature alpha-beta T cell)
0000084 (T cell)
0000789 (alpha-beta T cell)
0002419 (mature T cell)
0000624 (CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000363 (6 hr sample)
0000409 (T cell expansion sample)
0011446 (CD4-positiveCD25-CD44- naive conventional T cells stimulated with alphaCD3_CD28 - 06hr- (C57BL_6J) 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)
CL:0000051 (common lymphoid progenitor)
CL:0000790 (immature alpha-beta T cell)
CL:0002425 (early T lineage precursor)
CL:0002427 (resting double-positive thymocyte)