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|name=Universal RNA - Mouse Normal Tissues Biochain, pool1
|name=Universal RNA - Mouse Normal Tissues Biochain, pool1
|sample_id=10008
|sample_id=10008
|rna_tube_id=101B7
|rna_tube_id=101B6
|rna_box=101
|rna_box=101
|rna_position=B7
|rna_position=B6
|sample_cell_lot=NA
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_cell_catalog=NA
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=100.00000
|rna_weight_ug=100
|rna_concentration=
|rna_concentration=1
|sample_note=
|sample_note=
|profile_hcage=CNhs10613,LSID656,release008,COMPLETED
|profile_hcage=CNhs10613,LSID656,release008,COMPLETED

Revision as of 17:59, 27 February 2012


Name:Universal RNA - Mouse Normal Tissues Biochain, pool1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/C
tissuewhole body
dev stage6-8 weeks old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB307206
catalog numberCat:R4334566-1
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

CNhs10613

00.196
10.047
100
1000
10000.163
1001-0.0121
1002-0.0475
10030.00475
10040
10050.261
10060.252
1007-0.0772
10081.686
10090.0312
101-0.0509
10100
10110.0975
10120
10130.349
1014-0.0851
1015-0.237
1016-0.251
10170
10180.227
10190.047
1020
10200
1021-0.00173
10220.439
10230
10240.0834
10250.246
10260.255
10270.0141
10280
1029-0.0678
103-0.03
10300.047
1031-0.325
10320.174
10330.0141
10340.395
10350.047
1036-0.272
10370.128
1038-0.0576
10390.423
1040.047
1040-0.126
10410.353



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: CNhs10613

Jaspar motifP-value
MA0002.20.0871
MA0003.10.0227
MA0004.10.817
MA0006.10.255
MA0007.10.0366
MA0009.10.264
MA0014.10.617
MA0017.12.23801e-19
MA0018.20.819
MA0019.10.941
MA0024.10.0065
MA0025.10.0225
MA0027.10.186
MA0028.10.0665
MA0029.10.577
MA0030.10.035
MA0031.10.0166
MA0035.20.0282
MA0038.10.594
MA0039.20.087
MA0040.10.0943
MA0041.10.291
MA0042.10.719
MA0043.10.371
MA0046.11.05311e-86
MA0047.22.05608e-4
MA0048.10.902
MA0050.10.495
MA0051.10.162
MA0052.10.363
MA0055.10.94
MA0057.10.367
MA0058.10.964
MA0059.10.448
MA0060.10.327
MA0061.10.923
MA0062.20.00122
MA0065.23.06091e-16
MA0066.10.104
MA0067.10.413
MA0068.10.81
MA0069.10.499
MA0070.10.857
MA0071.10.0476
MA0072.10.563
MA0073.10.965
MA0074.10.373
MA0076.10.0183
MA0077.10.937
MA0078.10.0499
MA0079.20.261
MA0080.20.771
MA0081.10.0469
MA0083.10.737
MA0084.10.73
MA0087.10.948
MA0088.10.638
MA0090.10.176
MA0091.10.84
MA0092.10.334
MA0093.10.959
MA0099.20.84
MA0100.15.62472e-4
MA0101.10.292
MA0102.20.841
MA0103.10.00259
MA0104.20.714
MA0105.10.232
MA0106.10.948
MA0107.10.173
MA0108.29.36828e-5
MA0111.10.412
MA0112.22.3113e-6
MA0113.10.123
MA0114.14.07977e-19
MA0115.12.63916e-12
MA0116.10.102
MA0117.10.782
MA0119.10.0234
MA0122.10.998
MA0124.10.332
MA0125.10.195
MA0131.10.555
MA0135.10.7
MA0136.10.174
MA0137.20.7
MA0138.20.0153
MA0139.10.274
MA0140.10.413
MA0141.18.21654e-5
MA0142.10.805
MA0143.10.127
MA0144.10.5
MA0145.10.0251
MA0146.10.0411
MA0147.10.71
MA0148.11.01109e-4
MA0149.10.168
MA0150.10.125
MA0152.10.689
MA0153.14.56784e-52
MA0154.10.0365
MA0155.10.388
MA0156.10.0557
MA0157.10.0683
MA0159.10.00336
MA0160.19.37665e-6
MA0162.10.195
MA0163.10.00111
MA0164.10.629
MA0258.11.17331e-4
MA0259.10.588



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: CNhs10613

Novel motifP-value
10.148
100.367
1000.541
1010.304
1020.598
1030.163
1040.345
1050.608
1060.0365
1070.0696
1080.769
1090.0937
110.112
1100.149
1110.143
1120.0194
1130.638
1140.0265
1150.523
1160.159
1170.381
1180.436
1190.126
120.756
1200.588
1210.0966
1220.461
1230.636
1240.974
1250.902
1260.225
1270.794
1280.0775
1290.701
130.0263
1300.908
1310.409
1320.362
1330.447
1340.93
1350.372
1360.143
1370.949
1380.855
1390.0513
140.549
1400.962
1410.747
1420.908
1430.837
1440.929
1450.0897
1460.204
1470.477
1480.982
1490.47
150.172
1500.232
1510.322
1520.0902
1530.856
1540.811
1550.823
1567.11735e-11
1570.564
1580.243
1590.334
1600.472
1610.383
1620.248
1630.93
1640.369
1650.617
1660.516
1670.993
1680.539
1696.68224e-4
170.071
180.866
190.0566
20.52
200.978
210.651
220.146
230.26
240.0563
250.424
260.0772
270.699
280.333
290.332
30.179
300.474
310.363
320.0385
330.447
340.47
350.322
360.18
370.128
380.69
390.332
40.829
400.0802
410.0195
420.518
430.151
440.0708
450.297
460.191
470.14
480.137
490.164
50.266
500.67
510.536
520.159
530.99
540.496
550.764
560.6
570.944
580.204
590.0835
60.897
600.102
610.642
620.0971
630.11
640.476
650.441
660.795
670.164
680.189
690.981
70.198
700.0464
710.162
720.36
730.16
740.323
750.107
760.707
770.108
780.525
790.728
80.00662
800.491
810.829
820.0408
830.209
840.183
850.0257
860.22
870.0152
880.643
890.117
90.702
900.236
910.217
920.177
930.923
940.901
950.21
960.484
970.0779
980.337
990.0921



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: CNhs10613


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

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

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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