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{{f5samples
 
{{f5samples
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|id=FF:10582-108C6
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|F5samples=
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|name=
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|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
−
|sample_id=10582
 
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|rna_tube_id=108C6
 
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|rna_box=108
 
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|rna_position=C6
 
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|sample_cell_lot=
 
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|sample_cell_catalog=RCB0395
 
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|sample_company=RIKEN Bioresource centre
 
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|rna_lot_number=
 
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|rna_catalog_number=
 
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|sample_species=Human (Homo sapiens)
 
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|sample_strain=
 
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|sample_dev_stage=
 
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|sample_tissue=skin
 
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|sample_donor(cell lot)=
 
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|sample_sex=female
 
−
|sample_age=unknown
 
−
|sample_ethnicity=J
 
−
|rna_rin=
 
−
|rna_od260/230=2.12
 
−
|rna_od260/280=2.15
 
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|sample_cell_type=fibroblast
 
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|sample_cell_line=NCU-F8
 
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|sample_collaboration=Yukio Nakamura (RIKEN BRC)
 
−
|sample_experimental_condition=
 
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|sample_disease=Wilson's disease
 
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|rna_sample_type=total RNA
 
−
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 
−
|rna_weight_ug=24.11899
 
−
|rna_concentration=0.51317
 
−
|sample_note=
 
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|profile_hcage=,,,IN_LIBRARIAN
 
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|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
 
|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
−
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
 
 
|ancestors_in_disease_facet=DOID:0014667,DOID:3118,DOID:4,DOID:409,DOID:655,DOID:7,DOID:77,DOID:893,DOID:896
 
|ancestors_in_disease_facet=DOID:0014667,DOID:3118,DOID:4,DOID:409,DOID:655,DOID:7,DOID:77,DOID:893,DOID:896
−
|sample_description=
+
|comment=
 +
|created_by=
 +
|creation_date=
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|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=
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|top_motifs=
 
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|comment=
 
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|created_by=
 
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|creation_date=
 
−
|def=
 
 
|has_quality=
 
|has_quality=
 +
|id=FF:10582-108C6
 
|is_a=DOID:893;;EFO:0002091;;FF:0000210;;FF:0100453
 
|is_a=DOID:893;;EFO:0002091;;FF:0000210;;FF:0100453
 +
|name=
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 +
|profile_cagescan=
 +
|profile_hcage=,,,IN_LIBRARIAN
 +
|profile_rnaseq=
 +
|profile_srnaseq=
 +
|rna_box=108
 +
|rna_catalog_number=
 +
|rna_concentration=0.51317
 +
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 +
|rna_lot_number=
 +
|rna_od260/230=2.12
 +
|rna_od260/280=2.15
 +
|rna_position=C6
 +
|rna_rin=
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=108C6
 +
|rna_weight_ug=24.11899
 +
|sample_age=unknown
 +
|sample_cell_catalog=RCB0395
 +
|sample_cell_line=NCU-F8
 +
|sample_cell_lot=
 +
|sample_cell_type=fibroblast
 +
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
 +
|sample_company=RIKEN Bioresource centre
 +
|sample_description=
 +
|sample_dev_stage=
 +
|sample_disease=Wilson's disease
 +
|sample_donor(cell lot)=
 +
|sample_ethnicity=J
 +
|sample_experimental_condition=
 +
|sample_id=10582
 +
|sample_note=
 +
|sample_sex=female
 +
|sample_species=Human (Homo sapiens)
 +
|sample_strain=
 +
|sample_tissue=skin
 +
|top_motifs=
 
}}
 
}}

Revision as of 05:10, 21 March 2012


Name:
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stageNA
sexfemale
ageunknown
cell typefibroblast
cell lineNCU-F8
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
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>data

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



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



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>


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)

DOID: Disease
0014667 (disease of metabolism)
3118 (hepatobiliary disease)
4 (disease)
409 (liver disease)
655 (inherited metabolic disorder)
7 (disease of anatomical entity)
77 (gastrointestinal system disease)
893 (Wilson disease)
896 (metal metabolism disorder)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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