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{{f5samples
{{f5samples
|id=FF:11728-123D9
|id=FF:11728-123D9
|name=Mouse Schwann, donor1
|name=Schwann, donor1
|sample_id=11728
|sample_id=11728
|rna_tube_id=123D9
|rna_tube_id=123D9
Line 9: Line 9:
|sample_cell_catalog=N/A
|sample_cell_catalog=N/A
|sample_company=Sciencell/3H
|sample_company=Sciencell/3H
|rna_lot_number=3481.00000
|rna_lot_number=3481
|rna_catalog_number=M4100
|rna_catalog_number=M4100
|sample_species=Mouse (Mus musculus)
|sample_species=Mouse (Mus musculus)
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.75000
|rna_od260/230=1.75
|rna_od260/280=2.03000
|rna_od260/280=2.03
|sample_cell_type=schwann cell
|sample_cell_type=schwann cell
|sample_cell_line=
|sample_cell_line=
Line 32: Line 32:
|rna_concentration=0.21693
|rna_concentration=0.21693
|sample_note=
|sample_note=
|profile_hcage=CNhs12507,LSID918,release012,MAPPING
|profile_hcage=CNhs12507,LSID918,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:49, 27 February 2012


Name:Schwann, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueperipheral nervous system
dev stageNA
sexNA
ageNA
cell typeschwann cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3481
catalog numberM4100
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

CNhs12507

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.0166
1003-0.139
10040
10050
1006-0.0354
1007-0.0379
10080
1009-0.0751
1010.242
10100
1011-0.152
10120
1013-0.0322
10140
10150.0721
1016-0.0508
10170
10180
10190
1020
10200
10210.0317
1022-0.315
10230.0317
1024-0.216
1025-0.0294
10260
10270.0436
10280
1029-0.151
103-0.057
10300
1031-0.283
10320.0523
10330
10340
10350
10360.1
10370
10380.0314
1039-0.208
1040
1040-0.0865
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: CNhs12507

Jaspar motifP-value
MA0002.20.422
MA0003.10.421
MA0004.10.0101
MA0006.10.276
MA0007.10.0181
MA0009.10.134
MA0014.10.222
MA0017.10.0152
MA0018.21.5743e-5
MA0019.10.304
MA0024.10.074
MA0025.10.349
MA0027.10.313
MA0028.15.72349e-9
MA0029.10.384
MA0030.10.261
MA0031.10.571
MA0035.20.147
MA0038.10.615
MA0039.20.277
MA0040.10.987
MA0041.10.564
MA0042.10.625
MA0043.10.134
MA0046.15.12592e-14
MA0047.20.0139
MA0048.10.0615
MA0050.10.167
MA0051.10.551
MA0052.10.535
MA0055.13.52517e-4
MA0057.10.122
MA0058.13.27512e-5
MA0059.10.0373
MA0060.11.43335e-7
MA0061.10.812
MA0062.29.11733e-14
MA0065.20.19
MA0066.10.981
MA0067.18.88067e-4
MA0068.10.384
MA0069.10.172
MA0070.10.412
MA0071.10.925
MA0072.10.793
MA0073.10.42
MA0074.10.659
MA0076.11.51099e-9
MA0077.10.34
MA0078.12.94448e-4
MA0079.20.126
MA0080.20.509
MA0081.10.231
MA0083.10.201
MA0084.10.492
MA0087.10.336
MA0088.10.103
MA0090.10.26
MA0091.10.791
MA0092.10.732
MA0093.10.00981
MA0099.25.86959e-25
MA0100.10.513
MA0101.10.0644
MA0102.20.939
MA0103.12.59116e-4
MA0104.20.00366
MA0105.10.0196
MA0106.10.183
MA0107.10.0978
MA0108.20.00812
MA0111.10.185
MA0112.20.213
MA0113.10.203
MA0114.10.00197
MA0115.10.746
MA0116.10.00979
MA0117.10.0857
MA0119.10.251
MA0122.10.243
MA0124.10.821
MA0125.10.21
MA0131.10.0676
MA0135.10.4
MA0136.10.00211
MA0137.20.00966
MA0138.20.023
MA0139.10.0145
MA0140.10.111
MA0141.10.721
MA0142.10.733
MA0143.10.686
MA0144.10.195
MA0145.10.754
MA0146.10.666
MA0147.10.00759
MA0148.10.0022
MA0149.10.0038
MA0150.12.9413e-6
MA0152.10.33
MA0153.11.01511e-7
MA0154.10.2
MA0155.10.0944
MA0156.13.0797e-4
MA0157.10.674
MA0159.10.792
MA0160.10.432
MA0162.10.831
MA0163.10.0495
MA0164.10.545
MA0258.10.699
MA0259.10.0526



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: CNhs12507

Novel motifP-value
10.968
100.947
1000.895
1010.0323
1020.534
1030.114
1040.61
1050.531
1060.405
1070.095
1080.81
1090.952
110.839
1100.733
1110.353
1120.633
1130.725
1140.307
1150.674
1160.939
1170.205
1180.595
1190.381
120.906
1200.544
1210.432
1220.168
1230.7
1240.301
1250.53
1260.45
1270.0508
1280.246
1290.335
130.672
1300.0597
1310.712
1320.0853
1330.766
1340.158
1350.0216
1360.226
1370.974
1380.878
1390.112
140.353
1400.377
1410.228
1420.866
1430.199
1440.862
1450.654
1460.558
1470.248
1480.595
1490.649
150.126
1500.529
1510.771
1520.775
1530.731
1540.954
1550.584
1562.06401e-8
1570.786
1580.218
1590.0176
1600.00299
1610.835
1620.274
1630.454
1640.95
1650.728
1660.0498
1670.362
1680.0853
1690.54
170.902
180.133
190.134
20.0538
200.0181
210.699
220.54
230.0818
240.942
250.774
260.946
270.0198
280.755
290.216
30.844
300.223
310.768
320.155
330.844
340.192
350.365
360.152
370.156
380.53
390.979
40.958
400.398
410.0629
420.562
430.74
440.949
450.641
460.611
470.886
480.885
490.722
50.529
500.793
510.689
520.211
530.203
540.804
550.797
560.751
570.637
580.454
590.186
60.396
600.495
610.713
620.673
630.998
640.355
650.436
660.499
670.397
680.926
690.884
70.754
700.0607
710.964
720.903
730.133
740.52
750.933
760.0233
770.82
780.616
790.638
80.468
800.952
810.582
820.134
830.03
840.928
850.742
860.752
870.0249
880.753
890.67
90.263
900.36
910.31
920.522
930.97
940.755
950.0164
960.245
970.545
980.162
990.0836



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: CNhs12507


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)
0000030 (glioblast)
0000055 (non-terminally differentiated cell)
0000095 (neuron associated cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000133 (neurectodermal cell)
0000215 (barrier cell)
0000217 (insulating cell)
0000218 (myelinating Schwann cell;;Schwann cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000243 (glial cell (sensu Vertebrata))
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000328 (myelin accumulating cell)
0000333 (migratory neural crest cell)
0000339 (glioblast (sensu Vertebrata))
0000548 (animal cell)
0000630 (supportive cell)
0000692 (terminal Schwann cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002375 (Schwann cell precursor)
0002376 (non-myelinating Schwann cell)
0002377 (immature Schwann cell)
0002573 (Schwann cell)

UBERON: Anatomy
0000010 (peripheral 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)
0001062 (anatomical entity)
0002050 (embryonic structure)
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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