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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=0.81000
|rna_concentration=0.81
|sample_note=
|sample_note=
|profile_hcage=CNhs12638,LSID952,release012,COMPLETED
|profile_hcage=CNhs12638,LSID952,release012,COMPLETED

Revision as of 17:49, 27 February 2012


Name:Mouse Neurons - ventral spinal cord, donor2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespinal cord
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNASPI2
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

CNhs12638

00
10.601
100
1000.154
10000.0189
1001-0.0668
10020.099
10030.157
10040
10050
10060.497
1007-0.148
10080
1009-0.0912
101-0.0689
10100
10110.233
10120.0578
10130.116
10140.111
10150.213
10160.23
10170
10180
10190
1020
10200.569
10210.106
10220.0305
10230
10240.0247
10250.0933
10260
10270.384
10280
1029-0.0672
1030.0578
10300
1031-0.115
10320.281
10330
10340
10350.109
1036-0.135
10370
10380.0523
1039-0.0181
1040
1040-0.242
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: CNhs12638

Jaspar motifP-value
MA0002.21.03738e-4
MA0003.10.272
MA0004.10.398
MA0006.10.169
MA0007.10.178
MA0009.10.635
MA0014.10.515
MA0017.16.6315e-7
MA0018.20.153
MA0019.10.529
MA0024.10.772
MA0025.10.584
MA0027.10.255
MA0028.10.0752
MA0029.10.898
MA0030.10.212
MA0031.10.00795
MA0035.20.00554
MA0038.10.281
MA0039.20.0344
MA0040.10.244
MA0041.10.23
MA0042.10.614
MA0043.10.654
MA0046.11.43442e-13
MA0047.28.2378e-7
MA0048.10.13
MA0050.18.60437e-6
MA0051.12.07095e-4
MA0052.10.105
MA0055.10.0684
MA0057.10.269
MA0058.10.38
MA0059.10.189
MA0060.10.126
MA0061.10.0829
MA0062.25.57477e-4
MA0065.22.75961e-6
MA0066.10.0505
MA0067.10.715
MA0068.10.561
MA0069.10.121
MA0070.10.399
MA0071.10.0621
MA0072.10.047
MA0073.10.991
MA0074.10.126
MA0076.10.164
MA0077.10.315
MA0078.10.72
MA0079.20.385
MA0080.21.2721e-10
MA0081.10.272
MA0083.10.149
MA0084.10.578
MA0087.10.299
MA0088.10.171
MA0090.10.0819
MA0091.10.233
MA0092.10.202
MA0093.10.435
MA0099.21.03833e-4
MA0100.10.273
MA0101.10.0486
MA0102.20.64
MA0103.10.0842
MA0104.20.876
MA0105.10.0525
MA0106.10.089
MA0107.10.0883
MA0108.20.0602
MA0111.10.94
MA0112.21.78424e-4
MA0113.10.131
MA0114.17.52876e-6
MA0115.16.38204e-5
MA0116.10.0879
MA0117.10.628
MA0119.10.125
MA0122.10.979
MA0124.10.941
MA0125.10.205
MA0131.10.886
MA0135.10.997
MA0136.12.39575e-13
MA0137.20.15
MA0138.20.0277
MA0139.10.418
MA0140.12.5467e-4
MA0141.10.00361
MA0142.10.325
MA0143.10.667
MA0144.10.0619
MA0145.10.0443
MA0146.10.0165
MA0147.10.718
MA0148.17.50798e-7
MA0149.10.0587
MA0150.10.0146
MA0152.10.0504
MA0153.12.5904e-13
MA0154.10.0325
MA0155.10.713
MA0156.11.28954e-8
MA0157.10.0158
MA0159.10.00183
MA0160.10.0164
MA0162.10.277
MA0163.19.28277e-4
MA0164.10.961
MA0258.10.00775
MA0259.10.975



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: CNhs12638

Novel motifP-value
10.133
100.0782
1000.604
1010.792
1020.951
1030.0727
1040.609
1050.22
1060.0383
1070.124
1080.412
1090.00653
110.0645
1100.0474
1110.0573
1120.00279
1130.838
1140.105
1150.754
1160.694
1170.00687
1180.294
1190.0836
120.966
1200.322
1210.0805
1220.555
1230.0126
1240.248
1250.552
1260.0575
1270.0792
1280.0319
1290.118
137.75192e-6
1300.23
1310.535
1320.767
1330.994
1340.356
1350.301
1360.123
1370.733
1380.91
1390.167
140.762
1400.152
1410.381
1420.481
1430.409
1440.875
1450.00283
1460.249
1470.511
1480.534
1490.35
150.0882
1500.099
1510.441
1520.0788
1530.387
1540.788
1550.489
1568.79606e-5
1570.278
1580.025
1590.0538
1600.263
1610.132
1620.826
1630.307
1640.0132
1650.0606
1660.921
1670.59
1680.786
1690.00183
170.032
180.965
190.122
20.906
200.105
210.378
220.114
230.448
240.0318
250.66
261.0795e-6
270.715
280.537
290.0527
30.0673
300.959
310.933
320.794
330.102
340.739
350.984
360.339
370.0244
380.358
390.381
40.441
400.252
410.313
420.17
430.115
440.774
450.594
460.053
470.197
480.123
490.12
50.111
500.31
510.651
520.331
530.898
540.762
550.952
560.449
570.633
580.226
590.112
60.921
600.0343
610.0935
620.101
630.113
640.591
650.225
660.739
670.695
680.507
690.375
70.0215
700.0141
710.00954
720.532
730.0234
740.772
750.0488
760.518
770.355
780.0111
790.29
80.0802
800.606
810.937
820.234
830.057
840.512
850.0856
860.156
870.26
880.213
890.245
90.373
900.0848
910.275
920.359
930.0222
940.689
950.0384
960.155
970.922
980.404
990.609



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: CNhs12638


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)
0000117 (CNS neuron (sensu Vertebrata))
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000337 (neuroblast (sensu Vertebrata))
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)
0002612 (neuron of the ventral spinal cord)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001137 (dorsum)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0002050 (embryonic structure)
0002100 (trunk)
0002240 (spinal cord)
0002257 (ventral horn of spinal cord)
0002315 (gray matter of spinal cord)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0003103 (compound organ)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005174 (dorsal region element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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