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{{f5samples
{{f5samples
|id=FF:14311-155C9
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000055,UBERON:0000060,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000415,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000947,UBERON:0001009,UBERON:0001062,UBERON:0001637,UBERON:0001981,UBERON:0002049,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0003081,UBERON:0003509,UBERON:0003914,UBERON:0004111,UBERON:0004120,UBERON:0004535,UBERON:0004537,UBERON:0004571,UBERON:0004572,UBERON:0004573,UBERON:0004663,UBERON:0004664,UBERON:0004872,UBERON:0004923,UBERON:0005423,UBERON:0005734,UBERON:0005742,UBERON:0006965,UBERON:0007240,UBERON:0007500,UBERON:0007798
|name=Fibroblast - Aortic Adventitial, donor3 (nuclear fraction)
|sample_id=14311
|rna_tube_id=155C9
|rna_box=155
|rna_position=C9
|sample_cell_lot=lot:0000099514
|sample_cell_catalog=CC-7014
|sample_company=Lonza
|rna_lot_number=
|rna_catalog_number=N/A
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=19 years old adult
|sample_tissue=aorta
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=19
|sample_ethnicity=B
|rna_rin=
|rna_od260/230=2.15
|rna_od260/280=2.11
|sample_cell_type=fibroblast
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=nuclear RNA
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=43.67385
|rna_concentration=0.97053
|sample_note=
|profile_hcage=CNhs12400,LSID914,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371,CL:0002547,CL:1000306
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371,CL:0002547,CL:1000306
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000055,UBERON:0000060,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000415,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000947,UBERON:0001009,UBERON:0001062,UBERON:0001637,UBERON:0001981,UBERON:0002049,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0003081,UBERON:0003509,UBERON:0003914,UBERON:0004111,UBERON:0004120,UBERON:0004535,UBERON:0004537,UBERON:0004571,UBERON:0004572,UBERON:0004573,UBERON:0004663,UBERON:0004664,UBERON:0004872,UBERON:0004923,UBERON:0005423,UBERON:0005734,UBERON:0005742,UBERON:0006965,UBERON:0007240,UBERON:0007500,UBERON:0007798
|ancestors_in_disease_facet=
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|sample_description=
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|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:14311-155C9
|is_a=EFO:0002091;;FF:0000210;;FF:0000666
|is_a=EFO:0002091;;FF:0000210;;FF:0000666
|name=Fibroblast - Aortic Adventitial, donor3 (nuclear fraction)
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12400,LSID914,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=155
|rna_catalog_number=N/A
|rna_concentration=0.97053
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.15
|rna_od260/280=2.11
|rna_position=C9
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=155C9
|rna_weight_ug=43.67385
|sample_age=19
|sample_cell_catalog=CC-7014
|sample_cell_line=
|sample_cell_lot=lot:0000099514
|sample_cell_type=fibroblast
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Lonza
|sample_description=
|sample_dev_stage=19 years old adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=B
|sample_experimental_condition=nuclear RNA
|sample_id=14311
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=aorta
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}}
}}

Revision as of 15:32, 21 March 2012


Name:Fibroblast - Aortic Adventitial, donor3 (nuclear fraction)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueaorta
dev stage19 years old adult
sexfemale
age19
cell typefibroblast
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0.11
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs12400

Jaspar motifP-value
MA0002.20.00303
MA0003.10.85
MA0004.10.31
MA0006.10.881
MA0007.10.496
MA0009.10.159
MA0014.10.424
MA0017.10.00314
MA0018.20.251
MA0019.10.659
MA0024.10.739
MA0025.10.0403
MA0027.10.957
MA0028.10.764
MA0029.10.526
MA0030.10.397
MA0031.10.139
MA0035.20.059
MA0038.10.471
MA0039.20.345
MA0040.10.885
MA0041.10.565
MA0042.10.549
MA0043.10.128
MA0046.10.0544
MA0047.20.694
MA0048.10.181
MA0050.10.16
MA0051.10.276
MA0052.10.133
MA0055.10.764
MA0057.10.472
MA0058.10.252
MA0059.10.0679
MA0060.10.296
MA0061.17.72175e-4
MA0062.20.189
MA0065.23.8354e-4
MA0066.10.418
MA0067.10.366
MA0068.10.921
MA0069.10.487
MA0070.10.454
MA0071.10.189
MA0072.10.205
MA0073.10.752
MA0074.10.765
MA0076.10.456
MA0077.10.485
MA0078.10.691
MA0079.20.918
MA0080.21.74864e-9
MA0081.10.0395
MA0083.10.233
MA0084.10.159
MA0087.10.535
MA0088.10.326
MA0090.10.00508
MA0091.10.557
MA0092.10.438
MA0093.10.39
MA0099.20.00284
MA0100.10.892
MA0101.10.0051
MA0102.20.488
MA0103.13.41037e-4
MA0104.20.0316
MA0105.14.93609e-6
MA0106.10.931
MA0107.10.00316
MA0108.20.774
MA0111.10.344
MA0112.20.273
MA0113.10.701
MA0114.10.0061
MA0115.10.0272
MA0116.10.393
MA0117.10.637
MA0119.10.844
MA0122.10.394
MA0124.10.0107
MA0125.10.293
MA0131.10.642
MA0135.10.437
MA0136.11.51923e-9
MA0137.20.544
MA0138.20.0915
MA0139.10.816
MA0140.10.131
MA0141.10.0168
MA0142.10.0543
MA0143.10.517
MA0144.10.804
MA0145.10.333
MA0146.10.058
MA0147.10.12
MA0148.10.219
MA0149.10.214
MA0150.10.0325
MA0152.10.0412
MA0153.10.677
MA0154.10.0796
MA0155.10.675
MA0156.10.00197
MA0157.10.0903
MA0159.10.25
MA0160.10.00306
MA0162.10.287
MA0163.10.833
MA0164.10.711
MA0258.10.131
MA0259.10.379



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: CNhs12400

Novel motifP-value
10.0759
100.338
1000.929
1010.405
1020.358
1030.372
1040.994
1050.0536
1060.0131
1070.607
1080.591
1090.119
110.145
1100.803
1110.0193
1120.42
1130.0483
1140.103
1150.098
1160.912
1170.354
1180.44
1190.0738
120.416
1200.965
1210.93
1220.061
1230.00559
1240.0348
1250.174
1260.203
1270.0217
1280.0424
1290.213
130.335
1300.974
1310.893
1320.503
1330.853
1340.866
1350.312
1360.896
1370.564
1380.419
1390.175
140.348
1400.485
1410.783
1420.649
1430.0394
1440.809
1450.309
1460.459
1470.191
1480.0503
1490.279
150.0716
1500.82
1510.21
1520.173
1530.328
1540.902
1550.0406
1560.119
1570.562
1580.0583
1590.937
160.917
1600.0456
1610.742
1620.949
1630.718
1640.387
1650.724
1660.036
1670.192
1680.207
1690.425
170.461
180.553
190.602
20.624
200.864
210.899
220.662
230.756
240.199
250.0994
260.971
270.342
280.58
290.694
30.301
300.745
310.806
326.61488e-10
330.604
340.741
350.27
360.0137
370.404
380.225
390.919
40.135
400.0525
410.0442
420.146
430.234
440.792
450.48
460.323
470.155
480.402
490.0481
50.373
500.943
510.28
520.351
530.144
540.439
550.679
560.243
570.364
580.123
590.352
60.833
600.152
610.22
620.0609
630.488
640.182
650.255
660.244
670.814
680.584
690.589
70.0864
700.0575
710.398
720.355
730.201
740.422
750.287
760.701
770.717
780.0248
790.0714
80.204
800.187
810.431
820.0906
830.0537
840.558
850.391
860.784
870.838
880.522
890.652
90.9
900.0337
910.538
920.55
930.286
940.127
950.104
960.0426
970.258
980.00615
990.501



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: CNhs12400


FANTOM5 (FF) ontology

Direct parent terms


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)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002547 (fibroblast of the aortic adventitia)
1000306 (fibroblast of tunica adventitia of artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000415 (artery wall)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001062 (anatomical entity)
0001637 (artery)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004663 (aorta wall)
0004664 (aorta tunica adventitia)
0004872 (splanchnic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0005734 (tunica adventitia of blood vessel)
0005742 (adventitia)
0006965 (vascular cord)
0007240 (tunica adventitia of artery)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)

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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