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|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=12.00000
|rna_weight_ug=12
|rna_concentration=0.59000
|rna_concentration=0.59
|sample_note=
|sample_note=
|profile_hcage=CNhs13083,LSID1000,release012,COMPLETED
|profile_hcage=CNhs13083,LSID1000,release012,COMPLETED

Revision as of 17:49, 27 February 2012


Name:neurospheres - sympathetic neuron derived, biol_rep3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numbersym3
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

CNhs13083

00
10.0786
100
1000
1000-0.0355
1001-0.0749
1002-0.115
10030.032
10040
1005-0.123
10060.107
1007-0.0872
10080
10090.0874
101-0.00897
10100
10110.00247
10120
1013-0.072
1014-0.0851
10150.18
10160.297
10170
10180
10190
1020
10200.253
10210
1022-0.124
10230
1024-0.0899
1025-0.0161
10260.0198
10270.487
10280
1029-0.0989
103-0.0659
10300
10310.538
10320.018
10330.145
10340
10350
1036-0.0624
10370
10380.0617
1039-0.191
1040
10400.244
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: CNhs13083

Jaspar motifP-value
MA0002.23.66323e-5
MA0003.10.0319
MA0004.10.991
MA0006.10.432
MA0007.10.462
MA0009.10.0363
MA0014.10.816
MA0017.14.03421e-5
MA0018.28.96482e-4
MA0019.10.591
MA0024.10.0567
MA0025.10.839
MA0027.10.424
MA0028.10.832
MA0029.10.258
MA0030.10.817
MA0031.10.453
MA0035.20.00164
MA0038.10.0617
MA0039.20.447
MA0040.10.608
MA0041.10.157
MA0042.10.498
MA0043.10.0136
MA0046.12.96645e-12
MA0047.20.00786
MA0048.10.481
MA0050.10.00524
MA0051.10.0376
MA0052.10.00506
MA0055.10.405
MA0057.10.273
MA0058.10.689
MA0059.10.205
MA0060.11.05038e-4
MA0061.10.0452
MA0062.20.775
MA0065.21.75186e-5
MA0066.10.146
MA0067.10.362
MA0068.10.424
MA0069.10.376
MA0070.10.00314
MA0071.10.271
MA0072.10.272
MA0073.10.865
MA0074.10.442
MA0076.10.529
MA0077.10.042
MA0078.10.353
MA0079.20.306
MA0080.25.16925e-9
MA0081.10.613
MA0083.10.919
MA0084.10.845
MA0087.10.663
MA0088.10.667
MA0090.10.668
MA0091.10.757
MA0092.10.903
MA0093.10.928
MA0099.20.915
MA0100.10.742
MA0101.10.249
MA0102.20.85
MA0103.18.83727e-4
MA0104.20.744
MA0105.11.8065e-4
MA0106.10.198
MA0107.10.116
MA0108.20.00315
MA0111.10.567
MA0112.24.29685e-6
MA0113.10.195
MA0114.18.29929e-5
MA0115.10.0311
MA0116.18.38088e-4
MA0117.10.783
MA0119.10.178
MA0122.10.911
MA0124.11
MA0125.10.0466
MA0131.10.589
MA0135.10.249
MA0136.17.36297e-6
MA0137.20.689
MA0138.20.519
MA0139.10.079
MA0140.15.29e-5
MA0141.10.00327
MA0142.10.132
MA0143.10.127
MA0144.10.371
MA0145.10.0998
MA0146.10.434
MA0147.10.488
MA0148.10.00601
MA0149.10.932
MA0150.10.14
MA0152.10.632
MA0153.13.53354e-11
MA0154.10.00294
MA0155.10.383
MA0156.10.00355
MA0157.10.167
MA0159.10.0839
MA0160.10.0531
MA0162.10.207
MA0163.16.25396e-4
MA0164.10.878
MA0258.10.00384
MA0259.10.968



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: CNhs13083

Novel motifP-value
10.0674
100.0405
1000.857
1010.959
1020.9
1030.114
1040.944
1050.158
1060.03
1070.14
1080.95
1090.028
110.102
1100.117
1110.003
1120.0176
1130.537
1140.0675
1150.432
1160.377
1170.273
1180.427
1190.0363
120.483
1200.462
1210.249
1220.404
1230.357
1240.425
1250.865
1260.494
1270.28
1280.0523
1290.219
130.0152
1300.918
1310.846
1320.515
1330.952
1340.529
1350.767
1360.844
1370.431
1380.908
1390.182
140.54
1400.0209
1410.212
1420.568
1430.906
1440.939
1450.202
1460.521
1470.853
1480.694
1490.14
150.0866
1500.414
1510.426
1520.158
1530.898
1540.811
1550.941
1564.64134e-9
1570.081
1580.537
1590.112
1600.097
1610.338
1620.938
1630.619
1640.0856
1650.359
1660.72
1670.545
1680.751
1690.01
170.0536
180.677
190.172
20.645
200.516
210.341
220.276
230.304
240.135
250.357
260.0142
270.27
280.431
290.232
30.0747
300.758
310.682
320.0637
330.257
340.368
350.636
360.3
370.044
380.239
390.321
40.511
400.407
410.727
420.23
430.167
440.131
450.448
460.183
470.15
480.104
490.116
50.165
500.503
510.587
520.381
530.542
540.66
550.618
560.599
570.45
580.138
590.0389
60.552
600.0861
610.188
620.0432
630.0859
640.431
650.129
660.726
670.778
680.428
690.764
70.0474
700.007
710.0892
720.288
730.189
740.992
750.136
760.567
770.207
780.0878
790.123
80.0651
800.947
810.627
820.0215
830.149
840.669
850.0842
860.373
870.592
880.605
890.0804
90.444
900.346
910.255
920.139
930.581
940.383
950.113
960.403
970.71
980.144
990.211



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: CNhs13083


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)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000107 (autonomic neuron)
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000010 (peripheral nervous system)
0000013 (sympathetic nervous system)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002410 (autonomic nervous system)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
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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