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FF:11819-124F1

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Name:CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool2 (Balb_cAJcl)
Species:Mouse (Mus musculus)
Library ID:CNhs13225
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
strainBalb/cAJcl
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 numberBLTs3/28-6
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005688
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13225 CAGE DRX008794 DRR009666
Accession ID Mm9

Library idBAMCTSS
CNhs13225 DRZ001091 DRZ002476
Accession ID Mm10

Library idBAMCTSS
CNhs13225 DRZ012441 DRZ013826
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

CNhs13225

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0668
1002 --0.116
1003 --0.108
1004 0
1005 --0.024
1006 --0.424
1007 --0.11
1008 0
1009 --0.19
101 0.699
1010 0
1011 0.0336
1012 0.0333
1013 --0.254
1014 --0.0874
1015 0.344
1016 --0.594
1017 0
1018 0
1019 0
102 0.235
1020 0.0333
1021 0
1022 --0.224
1023 0
1024 --0.307
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0828
103 --0.0887
1030 0
1031 -1.193
1032 --0.576
1033 0.655
1034 0
1035 0
1036 0.568
1037 0
1038 --0.487
1039 --0.284
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: CNhs13225

Jaspar motif P-value
MA0002.2 0.00766
MA0003.1 0.337
MA0004.1 0.00368
MA0006.1 0.152
MA0007.1 0.372
MA0009.1 0.975
MA0014.1 0.772
MA0017.1 0.232
MA0018.2 0.0152
MA0019.1 0.63
MA0024.1 0.387
MA0025.1 0.932
MA0027.1 0.615
MA0028.1 7.31614e-8
MA0029.1 0.935
MA0030.1 0.119
MA0031.1 0.753
MA0035.2 0.863
MA0038.1 0.00594
MA0039.2 0.0361
MA0040.1 0.23
MA0041.1 0.126
MA0042.1 0.414
MA0043.1 0.0756
MA0046.1 1.031e-8
MA0047.2 0.778
MA0048.1 0.0961
MA0050.1 0.17
MA0051.1 0.379
MA0052.1 0.0594
MA0055.1 0.0123
MA0057.1 0.708
MA0058.1 0.00272
MA0059.1 3.48309e-7
MA0060.1 2.43015e-10
MA0061.1 1.41286e-4
MA0062.2 1.30098e-16
MA0065.2 0.0681
MA0066.1 0.203
MA0067.1 0.15
MA0068.1 0.635
MA0069.1 0.774
MA0070.1 0.283
MA0071.1 0.0859
MA0072.1 0.104
MA0073.1 0.771
MA0074.1 0.222
MA0076.1 7.07843e-9
MA0077.1 0.585
MA0078.1 0.19
MA0079.2 0.0264
MA0080.2 2.67505e-7
MA0081.1 0.00542
MA0083.1 0.138
MA0084.1 0.0979
MA0087.1 0.956
MA0088.1 0.334
MA0090.1 0.112
MA0091.1 0.236
MA0092.1 0.582
MA0093.1 0.00552
MA0099.2 0.0206
MA0100.1 0.187
MA0101.1 8.20456e-7
MA0102.2 0.41
MA0103.1 0.223
MA0104.2 2.64744e-6
MA0105.1 1.92748e-5
MA0106.1 0.629
MA0107.1 2.73302e-5
MA0108.2 1.80337e-5
MA0111.1 0.248
MA0112.2 0.0822
MA0113.1 0.245
MA0114.1 0.858
MA0115.1 0.0448
MA0116.1 0.0328
MA0117.1 0.547
MA0119.1 0.485
MA0122.1 0.757
MA0124.1 0.651
MA0125.1 0.0935
MA0131.1 0.296
MA0135.1 0.26
MA0136.1 2.33575e-15
MA0137.2 2.3372e-4
MA0138.2 0.0562
MA0139.1 0.355
MA0140.1 0.839
MA0141.1 0.0816
MA0142.1 0.426
MA0143.1 0.638
MA0144.1 0.0774
MA0145.1 0.186
MA0146.1 0.857
MA0147.1 3.74731e-8
MA0148.1 0.947
MA0149.1 0.0885
MA0150.1 0.066
MA0152.1 0.477
MA0153.1 1.43941e-4
MA0154.1 0.221
MA0155.1 0.876
MA0156.1 2.74252e-14
MA0157.1 0.973
MA0159.1 0.07
MA0160.1 0.0974
MA0162.1 0.872
MA0163.1 0.00265
MA0164.1 0.137
MA0258.1 0.0269
MA0259.1 0.012



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: CNhs13225

Novel motif P-value
1 0.126
10 0.038
100 0.482
101 0.55
102 0.366
103 0.386
104 0.413
105 0.64
106 0.554
107 0.798
108 0.882
109 0.163
11 0.113
110 0.0329
111 0.00466
112 0.0736
113 0.927
114 0.0434
115 0.952
116 0.722
117 4.54775e-4
118 0.504
119 0.463
12 0.423
120 0.198
121 0.487
122 0.978
123 0.802
124 0.264
125 0.0715
126 0.0884
127 0.504
128 0.427
129 0.496
13 0.0812
130 0.434
131 0.415
132 0.739
133 0.155
134 0.481
135 0.661
136 0.26
137 0.643
138 0.363
139 0.00302
14 0.212
140 0.075
141 0.328
142 0.261
143 0.023
144 0.303
145 0.0263
146 0.907
147 0.9
148 0.201
149 0.501
15 0.131
150 0.695
151 0.64
152 0.249
153 0.233
154 0.479
155 0.281
156 7.67826e-4
157 0.65
158 0.0161
159 0.787
160 0.794
161 0.0814
162 0.59
163 0.899
164 0.0142
165 0.494
166 0.0817
167 0.0226
168 0.857
169 0.668
17 0.552
18 0.0878
19 0.322
2 0.169
20 0.008
21 0.191
22 0.823
23 0.416
24 0.42
25 0.186
26 0.0276
27 0.577
28 0.582
29 0.0216
3 0.308
30 0.137
31 0.858
32 0.472
33 0.217
34 0.388
35 0.064
36 0.0436
37 0.204
38 0.941
39 0.896
4 0.584
40 0.396
41 0.143
42 0.426
43 0.545
44 0.276
45 0.472
46 0.145
47 0.379
48 0.155
49 0.148
5 0.0818
50 0.782
51 0.968
52 0.241
53 0.684
54 0.766
55 0.319
56 0.895
57 0.388
58 0.348
59 0.957
6 0.787
60 0.712
61 0.0816
62 0.0866
63 0.54
64 0.507
65 0.764
66 0.309
67 0.357
68 0.103
69 0.698
7 0.288
70 0.00311
71 0.0116
72 0.364
73 0.234
74 0.904
75 0.00961
76 0.00511
77 0.491
78 0.0489
79 0.388
8 0.0769
80 0.285
81 0.624
82 0.176
83 0.364
84 0.301
85 0.813
86 0.204
87 0.98
88 0.369
89 0.581
9 0.938
90 0.0208
91 0.935
92 0.103
93 0.214
94 0.195
95 0.133
96 0.0361
97 0.554
98 0.473
99 0.313



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: CNhs13225


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)
0011447 (CD4-positiveCD25-CD44- naive conventional T cells stimulated with alphaCD3_CD28- 06hr- (Balb_cAJcl) 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)