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{{f5samples
{{f5samples
|id=FF:11512-119G9
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000119,UBERON:0000383,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000490,UBERON:0000914,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001015,UBERON:0001062,UBERON:0001134,UBERON:0001558,UBERON:0002036,UBERON:0002050,UBERON:0002185,UBERON:0002204,UBERON:0002224,UBERON:0002329,UBERON:0002385,UBERON:0002532,UBERON:0003059,UBERON:0003077,UBERON:0003082,UBERON:0003104,UBERON:0004119,UBERON:0004120,UBERON:0004290,UBERON:0005178,UBERON:0005181,UBERON:0005291,UBERON:0005423,UBERON:0007023,UBERON:0007196,UBERON:0009142
|name=Smooth Muscle Cells - Bronchial, donor1
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|sample_company=Sciencell/3H
|rna_lot_number=lot:3982
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|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
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|sample_donor(cell lot)=
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|sample_cell_type=smooth muscle cell
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|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10
|rna_concentration=1.44
|sample_note=
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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:11512-119G9
|is_a=EFO:0002091;;FF:0000002;;FF:0000179;;FF:0000210;;FF:0000998
|is_a=EFO:0002091;;FF:0000002;;FF:0000179;;FF:0000210;;FF:0000998
|name=Smooth Muscle Cells - Bronchial, donor1
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11328,LSID768,release014,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10004,,,
|rna_box=119
|rna_catalog_number=SC3405
|rna_concentration=1.44
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=lot:3982
|rna_od260/230=
|rna_od260/280=
|rna_position=G9
|rna_rin=10
|rna_sample_type=total RNA
|rna_tube_id=119G9
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=smooth muscle cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Sciencell/3H
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11512
|sample_note=
|sample_sex=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=lung
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}}
}}

Revision as of 14:56, 21 March 2012


Name:Smooth Muscle Cells - Bronchial, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:3982
catalog numberSC3405
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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
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C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
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
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: CNhs11328

Jaspar motifP-value
MA0002.20.175
MA0003.10.285
MA0004.10.301
MA0006.10.439
MA0007.10.0453
MA0009.10.258
MA0014.10.984
MA0017.10.0862
MA0018.20.00167
MA0019.10.697
MA0024.10.0294
MA0025.10.113
MA0027.10.699
MA0028.10.017
MA0029.10.608
MA0030.10.218
MA0031.10.00469
MA0035.20.265
MA0038.10.386
MA0039.20.446
MA0040.10.241
MA0041.10.308
MA0042.10.772
MA0043.19.10403e-5
MA0046.10.0226
MA0047.20.675
MA0048.10.513
MA0050.11.26428e-6
MA0051.10.00183
MA0052.10.0123
MA0055.10.201
MA0057.10.133
MA0058.10.243
MA0059.10.215
MA0060.10.315
MA0061.10.733
MA0062.26.4049e-6
MA0065.20.033
MA0066.10.195
MA0067.10.0309
MA0068.10.462
MA0069.10.407
MA0070.10.00661
MA0071.10.0246
MA0072.10.767
MA0073.10.802
MA0074.10.221
MA0076.19.44043e-4
MA0077.10.362
MA0078.10.598
MA0079.20.89
MA0080.21.50633e-5
MA0081.10.0278
MA0083.19.13051e-8
MA0084.10.793
MA0087.10.746
MA0088.10.495
MA0090.10.0188
MA0091.10.00855
MA0092.10.132
MA0093.10.338
MA0099.23.86915e-4
MA0100.10.345
MA0101.10.604
MA0102.20.0117
MA0103.10.631
MA0104.20.745
MA0105.10.531
MA0106.10.0542
MA0107.10.7
MA0108.25.49168e-7
MA0111.10.369
MA0112.20.00407
MA0113.10.0517
MA0114.10.0921
MA0115.10.442
MA0116.10.299
MA0117.10.396
MA0119.10.0551
MA0122.10.891
MA0124.10.196
MA0125.10.952
MA0131.10.189
MA0135.10.18
MA0136.16.7214e-7
MA0137.20.00893
MA0138.20.324
MA0139.10.587
MA0140.10.425
MA0141.10.022
MA0142.10.814
MA0143.10.573
MA0144.10.513
MA0145.10.17
MA0146.10.0484
MA0147.10.648
MA0148.10.959
MA0149.10.491
MA0150.10.747
MA0152.10.548
MA0153.10.131
MA0154.10.159
MA0155.10.0769
MA0156.18.52834e-6
MA0157.10.0676
MA0159.10.571
MA0160.10.0579
MA0162.10.114
MA0163.10.164
MA0164.10.663
MA0258.10.0302
MA0259.10.795



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: CNhs11328

Novel motifP-value
10.67
100.791
1000.644
1010.753
1020.895
1030.404
1040.292
1050.124
1060.0407
1070.0261
1080.359
1090.068
110.046
1100.111
1110.764
1120.672
1130.466
1140.626
1150.4
1160.0815
1170.9
1180.684
1190.473
120.343
1200.336
1210.441
1220.616
1230.0593
1240.222
1250.366
1260.497
1270.384
1280.0389
1290.242
130.398
1300.149
1310.789
1320.221
1330.864
1340.212
1350.173
1360.509
1370.146
1380.344
1390.409
140.953
1400.512
1410.408
1420.781
1430.0421
1440.98
1450.151
1460.239
1470.386
1480.932
1490.036
150.901
1500.257
1510.478
1520.176
1530.402
1540.343
1550.4
1560.631
1570.0742
1580.151
1590.713
160.103
1600.0154
1610.592
1620.202
1630.706
1640.778
1650.237
1660.836
1670.268
1680.839
1690.0644
170.135
180.103
190.0537
20.23
200.477
210.464
220.0774
230.157
240.264
250.865
260.0244
270.228
280.303
290.973
30.441
300.166
310.261
321.18824e-5
330.359
340.139
350.968
360.881
370.27
380.386
390.222
40.314
400.0273
410.513
420.639
430.194
440.739
450.321
460.0896
470.32
480.24
490.178
50.924
500.394
510.284
520.365
530.822
540.251
550.533
560.231
570.231
580.799
590.0286
60.644
600.272
610.644
620.944
630.188
640.121
650.033
660.307
670.758
680.109
690.0352
70.748
700.099
710.127
720.858
730.103
740.92
750.795
760.49
770.0241
780.971
790.438
80.0451
800.643
810.521
820.452
830.89
840.501
850.159
860.875
870.442
880.223
890.202
90.183
900.0306
910.25
920.22
930.957
940.261
950.249
960.805
970.391
980.164
990.00262



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: CNhs11328


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)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000514 (smooth muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002598 (bronchial smooth muscle cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000119 (cell layer)
0000383 (musculature of body)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001558 (lower respiratory tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002185 (bronchus)
0002204 (musculoskeletal system)
0002224 (thoracic cavity)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007196 (tracheobronchial tree)
0009142 (entire embryonic mesenchyme)

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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