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{{f5samples
{{f5samples
|id=FF:11465-119B7
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000079,UBERON:0000119,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000490,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000990,UBERON:0001007,UBERON:0001015,UBERON:0001046,UBERON:0001062,UBERON:0001134,UBERON:0001353,UBERON:0001555,UBERON:0002036,UBERON:0002050,UBERON:0002204,UBERON:0002329,UBERON:0002367,UBERON:0002385,UBERON:0002530,UBERON:0002532,UBERON:0003059,UBERON:0003064,UBERON:0003077,UBERON:0003082,UBERON:0003101,UBERON:0003104,UBERON:0003353,UBERON:0003820,UBERON:0003929,UBERON:0003937,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004185,UBERON:0004290,UBERON:0004902,UBERON:0004921,UBERON:0005153,UBERON:0005156,UBERON:0005291,UBERON:0005399,UBERON:0005423,UBERON:0005911,UBERON:0006866,UBERON:0007026,UBERON:0009142
|name=Smooth Muscle Cells - Prostate, donor3
|sample_id=11465
|rna_tube_id=119B7
|rna_box=119
|rna_position=B7
|sample_cell_lot=
|sample_cell_catalog=C-14058
|sample_company=Promocell
|rna_lot_number=
|rna_catalog_number=N/A
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=prostate
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=0.79
|rna_od260/280=2.07
|sample_cell_type=smooth muscle cell
|sample_cell_line=
|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-miRNeasy_Mini-v1.0
|rna_weight_ug=5.8
|rna_concentration=0.233
|sample_note=
|profile_hcage=CNhs11910,LSID834,release010,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10010,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000056,CL:0000144,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000220,CL:0000222,CL:0000255,CL:0000355,CL:0000393,CL:0000514,CL:0000548,CL:0000680,CL:0000723,CL:0002321,CL:0002371,CL:1000487
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000056,CL:0000144,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000220,CL:0000222,CL:0000255,CL:0000355,CL:0000393,CL:0000514,CL:0000548,CL:0000680,CL:0000723,CL:0002321,CL:0002371,CL:1000487
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000079,UBERON:0000119,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000490,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000990,UBERON:0001007,UBERON:0001015,UBERON:0001046,UBERON:0001062,UBERON:0001134,UBERON:0001353,UBERON:0001555,UBERON:0002036,UBERON:0002050,UBERON:0002204,UBERON:0002329,UBERON:0002367,UBERON:0002385,UBERON:0002530,UBERON:0002532,UBERON:0003059,UBERON:0003064,UBERON:0003077,UBERON:0003082,UBERON:0003101,UBERON:0003104,UBERON:0003353,UBERON:0003820,UBERON:0003929,UBERON:0003937,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004185,UBERON:0004290,UBERON:0004902,UBERON:0004921,UBERON:0005153,UBERON:0005156,UBERON:0005291,UBERON:0005399,UBERON:0005423,UBERON:0005911,UBERON:0006866,UBERON:0007026,UBERON:0009142
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11465-119B7
|is_a=EFO:0002091;;FF:0000002;;FF:0000183;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000183;;FF:0000210
|name=Smooth Muscle Cells - Prostate, donor3
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11910,LSID834,release010,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10010,,,
|rna_box=119
|rna_catalog_number=N/A
|rna_concentration=0.233
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=0.79
|rna_od260/280=2.07
|rna_position=B7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=119B7
|rna_weight_ug=5.8
|sample_age=
|sample_cell_catalog=C-14058
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=smooth muscle cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Promocell
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11465
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=prostate
|top_motifs=
}}
}}

Revision as of 14:55, 21 March 2012


Name:Smooth Muscle Cells - Prostate, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueprostate
dev stageNA
sexmale
ageNA
cell typesmooth muscle cell
cell lineNA
companyPromocell
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>dataNo results for this sample

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: CNhs11910This sample isn't target for the analysis

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: CNhs11910This sample isn't target for the analysis

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: CNhs11910


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)
1000487 (smooth muscle cell of prostate)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000079 (male reproductive system)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0001007 (digestive system)
0001015 (musculature)
0001046 (hindgut)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001353 (anal region)
0001555 (digestive tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002367 (prostate gland)
0002385 (muscle tissue)
0002530 (gland)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003064 (intermediate mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003101 (male organism)
0003104 (mesenchyme)
0003353 (epithelium of hindgut)
0003820 (prostate bud)
0003929 (gut epithelium)
0003937 (sex gland)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004290 (dermomyotome)
0004902 (urogenital sinus epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006866 (terminal part of digestive tract)
0007026 (primitive gut)
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