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{{f5samples
{{f5samples
|id=FF:11924-125H7
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000930,UBERON:0001004,UBERON:0001007,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001828,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0004111,UBERON:0004119,UBERON:0005423,UBERON:0007026
|name=Fibroblast - Gingival, donor7 (control)
|sample_id=11924
|rna_tube_id=125H7
|rna_box=125
|rna_position=H7
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=APGF5-3
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=ANATOMICAL SYSTEM
|sample_donor(cell lot)=APGF5
|sample_sex=female
|sample_age=32
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.04
|rna_od260/280=2.06
|sample_cell_type=fibroblast
|sample_cell_line=
|sample_collaboration=Mitsuhiro Ohshima (Nihon University School of Dentistry)
|sample_experimental_condition=
|sample_disease=periodontitis
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=16.1464
|rna_concentration=1.61464
|sample_note=
|profile_hcage=CNhs14131,LSID1159,release016,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:0002552
|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:0002552
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000930,UBERON:0001004,UBERON:0001007,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001828,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0004111,UBERON:0004119,UBERON:0005423,UBERON:0007026
|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=
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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11924-125H7
|is_a=EFO:0002091;;FF:0000063
|is_a=EFO:0002091;;FF:0000063
|name=Fibroblast - Gingival, donor7 (control)
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs14131,LSID1159,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=125
|rna_catalog_number=
|rna_concentration=1.61464
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=APGF5-3
|rna_od260/230=2.04
|rna_od260/280=2.06
|rna_position=H7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=125H7
|rna_weight_ug=16.1464
|sample_age=32
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=fibroblast
|sample_collaboration=Mitsuhiro Ohshima (Nihon University School of Dentistry)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=periodontitis
|sample_donor(cell lot)=APGF5
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11924
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=ANATOMICAL SYSTEM
|top_motifs=
}}
}}

Revision as of 15:05, 21 March 2012


Name:Fibroblast - Gingival, donor7 (control)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexfemale
age32
cell typefibroblast
cell lineNA
companyNA
collaborationMitsuhiro Ohshima (Nihon University School of Dentistry)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberAPGF5-3
catalog numberNA
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: CNhs14131This 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: CNhs14131This 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: CNhs14131


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)
0002552 (fibroblast of gingiva)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001828 (gingiva)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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