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{{f5samples
{{f5samples
|id=FF:11816-124E7
|id=FF:11816-124E7
|name=CD4+CD25-CD44- naive conventional T cells stimulated with PMA an ionomycin, 02hr, pool1 (C57BL_6J)
|name=CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool1 (C57BL_6J)
|sample_id=11816
|sample_id=11816
|rna_tube_id=124E7
|rna_tube_id=124E7
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=2.05342
|rna_od260/230=2.053421369
|rna_od260/280=2.13014
|rna_od260/280=2.130136986
|sample_cell_type=T cell
|sample_cell_type=T cell
|sample_cell_line=
|sample_cell_line=
Line 32: Line 32:
|rna_concentration=0.13684
|rna_concentration=0.13684
|sample_note=
|sample_note=
|profile_hcage=CNhs13219,LSID1005,release012,MAPPING
|profile_hcage=CNhs13219,LSID1005,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:12, 27 February 2012


Name:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool1 (C57BL_6J)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
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 numberB6TsPI-2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs13219

00
10
100
1000
1000-0.0355
1001-0.0631
1002-0.116
1003-0.15
10040
1005-0.0747
1006-0.436
1007-0.223
10080
1009-0.19
1010.676
10100
10110.153
10120.00667
1013-0.323
1014-0.0279
10150.167
1016-0.594
10170
10180.0572
10190
1020.906
10200.108
10210.266
1022-0.281
10230.153
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.111
103-0.0887
10300
1031-1.09
1032-0.655
10330.949
10340
10350
10360.618
10370
1038-0.162
1039-0.441
1040
1040-0.216
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13219

Jaspar motifP-value
MA0002.20.0167
MA0003.10.103
MA0004.10.018
MA0006.10.154
MA0007.10.568
MA0009.10.555
MA0014.10.867
MA0017.10.19
MA0018.22.45043e-9
MA0019.10.825
MA0024.10.943
MA0025.10.297
MA0027.10.487
MA0028.10.00133
MA0029.10.765
MA0030.10.961
MA0031.10.28
MA0035.20.601
MA0038.10.0152
MA0039.20.106
MA0040.10.862
MA0041.10.0164
MA0042.10.176
MA0043.17.94709e-4
MA0046.11.01137e-11
MA0047.20.771
MA0048.10.192
MA0050.12.12062e-5
MA0051.10.00243
MA0052.10.953
MA0055.10.0937
MA0057.10.921
MA0058.10.00447
MA0059.11.28302e-4
MA0060.10.00203
MA0061.17.00791e-11
MA0062.21.51164e-11
MA0065.20.427
MA0066.10.582
MA0067.15.32808e-4
MA0068.15.19127e-5
MA0069.10.424
MA0070.10.845
MA0071.10.603
MA0072.10.0893
MA0073.10.515
MA0074.10.558
MA0076.10.00126
MA0077.10.543
MA0078.10.518
MA0079.20.263
MA0080.26.67227e-10
MA0081.10.0017
MA0083.10.873
MA0084.10.468
MA0087.10.873
MA0088.10.175
MA0090.10.0329
MA0091.10.766
MA0092.10.111
MA0093.10.0187
MA0099.21.79377e-6
MA0100.10.298
MA0101.15.73466e-16
MA0102.20.583
MA0103.10.644
MA0104.21.06591e-4
MA0105.11.43349e-6
MA0106.10.658
MA0107.15.90608e-16
MA0108.20.601
MA0111.10.449
MA0112.20.609
MA0113.10.885
MA0114.10.00737
MA0115.10.175
MA0116.10.937
MA0117.10.0252
MA0119.10.0407
MA0122.10.539
MA0124.10.954
MA0125.10.0857
MA0131.10.372
MA0135.10.765
MA0136.12.503e-18
MA0137.20.00456
MA0138.24.47061e-4
MA0139.10.267
MA0140.10.857
MA0141.10.705
MA0142.10.579
MA0143.10.156
MA0144.10.199
MA0145.10.028
MA0146.10.913
MA0147.16.24597e-6
MA0148.10.595
MA0149.10.227
MA0150.10.0344
MA0152.10.0561
MA0153.12.30202e-6
MA0154.10.862
MA0155.10.295
MA0156.12.29709e-15
MA0157.10.182
MA0159.10.854
MA0160.10.945
MA0162.10.0203
MA0163.10.531
MA0164.10.0365
MA0258.10.567
MA0259.10.0168



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13219

Novel motifP-value
10.851
100.194
1000.472
1010.474
1020.377
1030.289
1040.64
1050.455
1060.196
1070.892
1080.683
1090.873
110.637
1100.355
1110.141
1120.277
1130.824
1140.858
1150.735
1160.536
1173.10959e-4
1180.468
1190.878
120.396
1200.137
1210.308
1220.78
1230.544
1240.259
1250.514
1260.416
1270.488
1280.115
1290.64
130.109
1300.647
1310.242
1320.469
1330.125
1340.448
1350.173
1360.761
1370.776
1380.953
1390.189
140.084
1400.413
1410.967
1420.486
1430.0152
1440.425
1450.173
1460.832
1470.596
1480.138
1490.13
150.457
1500.836
1510.966
1520.544
1530.456
1540.143
1550.291
1560.698
1570.885
1580.0151
1590.535
1600.171
1610.237
1620.117
1630.749
1640.0464
1650.546
1660.199
1670.0674
1680.557
1690.277
170.856
180.252
190.0213
20.00797
200.00313
210.203
220.402
230.758
240.529
250.362
260.403
270.109
280.505
290.183
30.922
300.0986
310.479
320.0892
330.214
340.255
350.263
360.147
370.321
380.635
390.626
40.808
400.984
410.164
420.728
430.811
440.72
450.296
460.793
470.714
480.742
490.519
50.293
500.63
510.778
520.497
530.638
540.736
550.982
560.708
570.807
580.645
590.421
60.875
600.52
610.188
620.253
630.706
640.651
650.859
660.727
670.705
680.196
690.591
70.695
700.0152
710.174
720.806
730.432
740.735
750.0231
760.0247
770.0235
780.0322
790.858
80.856
800.42
810.827
820.9
830.169
840.242
850.513
860.17
870.604
880.552
890.433
90.842
900.376
910.616
920.515
930.146
940.422
950.534
960.426
970.556
980.758
990.0348



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13219


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000624 (CD4-positive, alpha-beta T cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000789 (alpha-beta T cell)
0000790 (immature alpha-beta T cell)
0000791 (mature alpha-beta T cell)
0000805 (immature single positive thymocyte)
0000806 (DN2 thymocyte)
0000807 (DN3 thymocyte)
0000808 (DN4 thymocyte)
0000809 (double-positive, alpha-beta thymocyte)
0000810 (CD4-positive, alpha-beta thymocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000893 (thymocyte)
0000894 (DN1 thymic pro-T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002419 (mature T cell)
0002420 (immature T cell)
0002425 (early T lineage precursor)
0002427 (resting double-positive thymocyte)
0002428 (double-positive blast)
0002429 (CD69-positive double-positive thymocyte)
0002431 (CD4-positive, CD8-intermediate double-positive thymocyte)
0002432 (CD24-positive, CD4 single-positive thymocyte)
0002433 (CD69-positive, CD4-positive single-positive thymocyte)
0002436 (mature CD4 single-positive thymocyte)
0002489 (double negative thymocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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