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|name=ST2 (Mesenchymal stem cells) cells, medium change (without induction), 00hr, biol_rep1 (000hC4)
|name=ST2 (Mesenchymal stem cells) cells, medium change (without induction), 00hr, biol_rep1 (000hC4)
|sample_id=12338
|sample_id=12338
|rna_tube_id=
|rna_tube_id=130I7
|rna_box=130
|rna_box=130
|rna_position=I7
|rna_position=I7
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=3.44200
|rna_od260/230=3.442
|rna_od260/280=2.11000
|rna_od260/280=2.11
|sample_cell_type=mesenchymal stem cell
|sample_cell_type=mesenchymal stem cell
|sample_cell_line=ST2
|sample_cell_line=ST2
Line 29: Line 29:
|rna_sample_type=
|rna_sample_type=
|rna_extraction_protocol=
|rna_extraction_protocol=
|rna_weight_ug=5.50000
|rna_weight_ug=5.50
|rna_concentration=0.29358
|rna_concentration=0.29
|sample_note=2039.00000
|sample_note=2039
|profile_hcage=CNhs11939,LSID835,release010,COMPLETED
|profile_hcage=CNhs11939,LSID835,release010,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,

Revision as of 17:54, 27 February 2012


Name:ST2 (Mesenchymal stem cells) cells, medium change (without induction), 00hr, biol_rep1 (000hC4)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineST2
companyNA
collaborationYasushi Okazaki (Saitama medical college)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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

CNhs11939

00
10
100
1000
10000.247
10010.0155
1002-0.116
10030.228
10040
10050
1006-0.0916
10070.00293
10080
10090.746
1010.0347
10100
1011-0.229
10120
10130.0165
1014-0.0874
10150.0378
10160.141
10170
10180
10190
1020
10200
1021-0.0487
1022-0.124
10230
1024-0.307
1025-0.0611
10260
1027-0.00273
10280.127
1029-0.151
1030.404
10300
1031-0.195
1032-0.115
10330.0157
10340
10350
10360.106
10370
10380.112
1039-0.0843
1040
10400.396
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: CNhs11939

Jaspar motifP-value
MA0002.20.136
MA0003.10.644
MA0004.10.282
MA0006.10.394
MA0007.10.853
MA0009.10.588
MA0014.10.32
MA0017.10.0165
MA0018.20.685
MA0019.10.52
MA0024.10.0412
MA0025.10.253
MA0027.10.454
MA0028.14.99891e-5
MA0029.10.61
MA0030.10.783
MA0031.10.636
MA0035.20.00121
MA0038.10.468
MA0039.20.289
MA0040.10.258
MA0041.10.664
MA0042.10.347
MA0043.10.36
MA0046.11.46058e-6
MA0047.20.709
MA0048.14.64156e-4
MA0050.10.216
MA0051.10.23
MA0052.18.49384e-4
MA0055.13.88065e-4
MA0057.10.135
MA0058.10.0621
MA0059.10.829
MA0060.10.834
MA0061.10.309
MA0062.23.48067e-6
MA0065.20.669
MA0066.10.44
MA0067.10.608
MA0068.10.362
MA0069.10.659
MA0070.10.152
MA0071.10.907
MA0072.10.899
MA0073.10.547
MA0074.10.745
MA0076.11.18221e-4
MA0077.10.401
MA0078.10.262
MA0079.20.641
MA0080.20.32
MA0081.10.983
MA0083.13.11196e-4
MA0084.10.552
MA0087.10.902
MA0088.11.1465e-4
MA0090.10.0179
MA0091.10.795
MA0092.10.352
MA0093.10.257
MA0099.21.73472e-7
MA0100.10.0798
MA0101.10.232
MA0102.20.471
MA0103.12.43676e-7
MA0104.20.629
MA0105.10.259
MA0106.11.71478e-4
MA0107.10.701
MA0108.20.00448
MA0111.10.149
MA0112.20.062
MA0113.10.772
MA0114.10.314
MA0115.10.22
MA0116.10.108
MA0117.10.294
MA0119.10.394
MA0122.10.699
MA0124.10.28
MA0125.10.0191
MA0131.10.603
MA0135.10.0407
MA0136.10.445
MA0137.20.00396
MA0138.21.00494e-4
MA0139.10.848
MA0140.19.79602e-5
MA0141.10.975
MA0142.10.0175
MA0143.10.857
MA0144.10.024
MA0145.10.235
MA0146.15.4912e-4
MA0147.10.473
MA0148.10.683
MA0149.10.198
MA0150.10.107
MA0152.10.0397
MA0153.14.8865e-6
MA0154.10.372
MA0155.10.761
MA0156.10.179
MA0157.10.738
MA0159.10.931
MA0160.10.781
MA0162.10.118
MA0163.10.666
MA0164.10.556
MA0258.10.751
MA0259.10.413



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: CNhs11939

Novel motifP-value
10.301
100.0391
1000.788
1010.276
1020.0974
1030.569
1040.962
1050.802
1060.904
1070.373
1080.523
1090.0698
110.167
1100.0373
1110.791
1120.947
1130.139
1140.911
1150.89
1160.344
1174.42548e-4
1180.907
1190.2
120.652
1200.232
1210.41
1220.32
1230.19
1240.213
1250.578
1260.549
1270.0773
1280.228
1290.818
130.0129
1300.612
1310.598
1320.227
1330.152
1340.901
1350.298
1360.293
1370.97
1380.595
1390.0109
140.428
1400.983
1410.725
1420.801
1430.206
1440.153
1450.266
1460.361
1470.516
1480.892
1490.0859
150.537
1500.0368
1510.942
1520.0821
1530.91
1540.403
1550.186
1561.19319e-28
1570.771
1580.543
1590.148
1600.931
1610.793
1620.814
1630.723
1640.00481
1650.529
1660.82
1670.111
1680.265
1690.00175
170.55
180.497
190.393
20.539
200.0564
210.0503
220.204
230.288
240.712
250.978
260.232
270.376
280.909
290.0182
30.261
300.471
310.282
320.563
330.277
340.765
350.138
360.302
370.0132
380.917
390.724
40.552
400.917
410.312
420.505
430.835
440.222
450.855
460.545
470.231
480.356
490.412
50.433
500.575
510.844
520.735
530.608
540.313
550.779
560.57
570.409
580.826
590.445
60.844
600.445
610.922
620.555
630.742
640.666
650.844
660.477
670.278
680.251
690.863
70.247
700.0477
710.00954
720.785
730.0094
740.813
750.0975
760.485
770.344
780.0108
790.713
80.639
800.0124
810.887
820.512
830.767
840.794
850.996
860.791
870.0191
880.384
890.262
90.67
900.0552
910.943
920.544
930.245
940.751
950.0121
960.749
970.384
980.248
990.746



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: CNhs11939


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)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic 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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