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|name=Mouse CD4+ T Cells, donor1
|name=Mouse CD4+ T Cells, donor1
|sample_id=11854
|sample_id=11854
|rna_tube_id=
|rna_tube_id=124I9
|rna_box=124
|rna_box=124
|rna_position=I9
|rna_position=I9
Line 12: Line 12:
|rna_catalog_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL_6
|sample_strain=
|sample_dev_stage=
|sample_dev_stage=
|sample_tissue=spleen
|sample_tissue=spleen
Line 29: Line 29:
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=5.26400
|rna_weight_ug=5.264
|rna_concentration=0.09400
|rna_concentration=0.094
|sample_note=
|sample_note=
|profile_hcage=CNhs13509,,,SEQUENCING QUEUE
|profile_hcage=CNhs13509,LSID1025,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:48, 27 February 2012


Name:Mouse CD4+ T Cells, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespleen
dev stageNA
sexNA
ageNA
cell typet cell, CD4+
cell lineNA
companyNA
collaborationKawamoto (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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

CNhs13509

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.123
10040
10050.116
1006-0.148
10070.032
10080
1009-0.19
1010.139
10100
10110.129
10120.186
1013-0.188
1014-0.0874
1015-0.0376
1016-0.594
10170
10180
10190
1020.729
10200
10210
1022-0.315
10230
1024-0.0899
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-1.148
1032-0.655
10330.427
10340
10350
10360.433
10370
10380.0211
1039-0.223
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: CNhs13509

Jaspar motifP-value
MA0002.23.97871e-5
MA0003.10.264
MA0004.10.0952
MA0006.10.434
MA0007.10.648
MA0009.10.71
MA0014.10.793
MA0017.10.357
MA0018.24.81796e-8
MA0019.10.79
MA0024.10.774
MA0025.10.644
MA0027.10.808
MA0028.12.303e-4
MA0029.10.506
MA0030.10.122
MA0031.12.07317e-4
MA0035.20.809
MA0038.17.6594e-4
MA0039.20.191
MA0040.10.164
MA0041.10.387
MA0042.10.511
MA0043.10.0193
MA0046.19.60373e-11
MA0047.20.0705
MA0048.10.504
MA0050.13.66975e-8
MA0051.11.93679e-5
MA0052.10.0857
MA0055.10.411
MA0057.10.911
MA0058.10.0525
MA0059.10.0967
MA0060.10.00865
MA0061.11.79873e-6
MA0062.21.82661e-18
MA0065.20.487
MA0066.10.21
MA0067.10.00178
MA0068.10.0105
MA0069.10.862
MA0070.10.87
MA0071.10.667
MA0072.10.0321
MA0073.10.772
MA0074.10.659
MA0076.11.01233e-5
MA0077.10.224
MA0078.10.541
MA0079.20.0862
MA0080.21.16003e-13
MA0081.10.00354
MA0083.10.245
MA0084.10.823
MA0087.10.871
MA0088.10.536
MA0090.10.0235
MA0091.10.987
MA0092.10.59
MA0093.10.118
MA0099.20.692
MA0100.10.111
MA0101.14.06577e-8
MA0102.20.863
MA0103.10.106
MA0104.20.123
MA0105.13.5427e-5
MA0106.10.821
MA0107.17.94176e-8
MA0108.20.0245
MA0111.10.354
MA0112.20.81
MA0113.10.587
MA0114.10.0194
MA0115.10.358
MA0116.10.481
MA0117.10.104
MA0119.10.11
MA0122.10.414
MA0124.10.516
MA0125.10.12
MA0131.10.537
MA0135.10.832
MA0136.17.22525e-25
MA0137.20.013
MA0138.20.00272
MA0139.10.567
MA0140.10.508
MA0141.10.488
MA0142.10.259
MA0143.10.35
MA0144.10.0904
MA0145.10.127
MA0146.10.549
MA0147.10.0656
MA0148.10.18
MA0149.10.0738
MA0150.10.669
MA0152.10.628
MA0153.12.54423e-6
MA0154.10.785
MA0155.10.351
MA0156.17.58134e-25
MA0157.14.2973e-4
MA0159.10.467
MA0160.10.913
MA0162.10.365
MA0163.10.162
MA0164.10.31
MA0258.10.182
MA0259.10.211



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: CNhs13509

Novel motifP-value
10.467
100.0592
1000.526
1010.995
1020.475
1030.486
1040.998
1050.569
1060.559
1070.487
1080.754
1090.504
110.415
1100.292
1110.328
1120.177
1130.444
1140.3
1150.608
1160.57
1172.97036e-4
1180.211
1190.656
120.239
1200.0611
1210.337
1220.97
1230.66
1240.465
1250.561
1260.456
1270.784
1280.246
1290.332
130.143
1300.71
1310.267
1320.828
1330.55
1340.592
1350.878
1360.546
1370.336
1380.267
1390.321
140.603
1400.528
1410.324
1420.263
1432.52455e-4
1440.507
1450.199
1460.784
1470.469
1480.178
1490.176
150.185
1500.881
1510.288
1520.379
1530.47
1540.166
1550.0504
1560.0661
1570.833
1580.0143
1590.805
1600.354
1610.185
1620.277
1630.32
1640.0919
1650.819
1660.487
1670.0943
1680.337
1690.625
170.855
180.224
190.0776
20.018
200.0211
210.0869
220.615
230.995
240.552
250.198
260.363
270.658
280.384
290.0651
30.522
300.119
310.597
320.146
330.0987
340.353
350.0339
360.0899
370.232
380.618
390.365
40.7
400.504
410.149
420.281
430.713
440.683
450.27
460.506
470.862
480.431
490.207
50.119
500.469
510.69
520.184
530.607
540.639
550.896
560.993
570.688
580.321
590.565
60.661
600.854
610.209
620.0923
630.995
640.993
650.407
660.451
670.698
680.439
690.737
70.555
700.0234
710.192
720.954
730.322
740.713
750.00795
760.0271
770.0257
780.0404
790.954
80.71
800.163
810.992
820.495
830.0946
840.925
850.847
860.158
870.542
880.37
890.664
90.923
900.102
910.718
920.643
930.111
940.282
950.367
960.41
970.459
980.467
990.0285



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: CNhs13509


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)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor 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)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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