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|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_weight_ug=10.00000
|rna_weight_ug=10
|rna_concentration=0.76000
|rna_concentration=0.76
|sample_note=
|sample_note=
|profile_hcage=CNhs12616,LSID952,release012,COMPLETED
|profile_hcage=CNhs12616,LSID952,release012,COMPLETED

Revision as of 17:48, 27 February 2012


Name:Mouse Mesenchymal stem cells - bone marrow derived, donor3
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 lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMCS3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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

CNhs12616

00
10
100
1000
10000
1001-0.0668
1002-0.0156
1003-0.0349
10040
10050
10060.212
1007-0.426
10080
1009-0.19
101-0.54
10100
10110
10120
10130.0678
1014-0.0874
10150.00844
1016-0.232
10170
10180
10190
1020
10200.658
10210.23
1022-0.0446
10230
1024-0.14
1025-0.0611
10260
10270
10280
1029-0.176
1030
10300
1031-0.243
1032-0.184
1033-0.0752
10340
10350
1036-0.185
10370
1038-0.14
1039-0.11
1040
1040-0.0211
10410.233



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: CNhs12616

Jaspar motifP-value
MA0002.25.06249e-6
MA0003.10.133
MA0004.10.414
MA0006.10.504
MA0007.10.628
MA0009.10.76
MA0014.10.698
MA0017.10.105
MA0018.20.12
MA0019.10.743
MA0024.10.00543
MA0025.10.483
MA0027.10.512
MA0028.10.573
MA0029.10.951
MA0030.10.211
MA0031.10.698
MA0035.20.382
MA0038.11.77467e-4
MA0039.20.782
MA0040.10.769
MA0041.10.479
MA0042.10.799
MA0043.10.146
MA0046.11.01955e-4
MA0047.20.723
MA0048.10.677
MA0050.13.89121e-6
MA0051.15.8423e-4
MA0052.10.0399
MA0055.10.987
MA0057.10.28
MA0058.10.26
MA0059.10.244
MA0060.17.57707e-13
MA0061.10.0303
MA0062.20.28
MA0065.20.00357
MA0066.10.0315
MA0067.10.698
MA0068.10.636
MA0069.10.741
MA0070.10.198
MA0071.10.138
MA0072.10.407
MA0073.10.592
MA0074.10.0174
MA0076.10.255
MA0077.10.516
MA0078.10.539
MA0079.20.566
MA0080.23.02804e-13
MA0081.10.00289
MA0083.10.405
MA0084.10.98
MA0087.10.527
MA0088.10.379
MA0090.10.8
MA0091.10.253
MA0092.10.394
MA0093.10.435
MA0099.24.10203e-4
MA0100.10.859
MA0101.10.141
MA0102.20.754
MA0103.10.706
MA0104.20.833
MA0105.10.00555
MA0106.10.22
MA0107.10.144
MA0108.20.181
MA0111.10.313
MA0112.29.40663e-5
MA0113.10.267
MA0114.10.251
MA0115.10.814
MA0116.10.00187
MA0117.10.875
MA0119.10.217
MA0122.10.502
MA0124.10.764
MA0125.10.074
MA0131.10.155
MA0135.10.681
MA0136.12.23736e-10
MA0137.20.738
MA0138.20.458
MA0139.10.108
MA0140.10.274
MA0141.10.0126
MA0142.10.816
MA0143.10.214
MA0144.10.415
MA0145.10.0506
MA0146.10.00606
MA0147.10.777
MA0148.10.641
MA0149.10.213
MA0150.10.0114
MA0152.10.245
MA0153.10.00269
MA0154.10.00452
MA0155.10.395
MA0156.10.00297
MA0157.10.667
MA0159.10.00298
MA0160.10.142
MA0162.10.202
MA0163.13.81235e-5
MA0164.10.959
MA0258.10.00667
MA0259.10.584



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: CNhs12616

Novel motifP-value
10.126
100.0691
1000.808
1010.968
1020.429
1030.118
1040.799
1050.552
1060.0215
1070.285
1080.393
1090.0227
110.0569
1100.085
1110.0483
1120.0938
1130.751
1140.0259
1150.435
1160.104
1170.0546
1180.421
1190.234
120.814
1200.0635
1210.453
1220.833
1230.607
1240.931
1250.277
1260.378
1270.241
1280.0377
1290.0984
130.11
1300.615
1310.108
1320.402
1330.131
1340.684
1350.855
1360.696
1370.49
1380.462
1390.284
140.48
1400.233
1410.254
1420.217
1430.0216
1440.93
1450.173
1460.624
1470.85
1480.0789
1490.0144
150.103
1500.147
1510.206
1520.0899
1530.79
1540.603
1550.408
1560.46
1570.567
1580.552
1590.846
1600.468
1610.0728
1620.783
1630.831
1640.182
1650.177
1660.673
1670.409
1680.517
1690.00641
170.0221
180.0909
190.159
20.522
200.36
210.336
220.11
230.116
240.106
250.762
260.0117
270.49
280.756
290.0694
30.0267
300.744
310.244
320.166
330.331
340.362
350.573
360.013
370.0397
380.192
390.689
40.31
400.0653
410.36
420.225
430.0486
440.0411
450.516
460.066
470.234
480.188
490.0743
50.253
500.483
510.805
520.467
530.978
540.737
550.581
560.196
570.418
580.387
590.0071
60.885
600.123
610.444
620.136
630.11
640.243
650.0355
660.728
670.158
680.00837
690.119
70.427
706.16872e-4
710.035
720.151
730.0357
740.725
750.0551
760.462
770.118
780.0475
790.651
80.0486
800.991
810.15
820.244
830.714
840.391
850.0771
860.449
870.209
880.9
890.0915
90.547
900.306
910.235
920.0871
930.418
940.496
950.048
960.567
970.839
980.0499
990.93



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: CNhs12616


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)
0002092 (bone marrow cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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