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{{f5samples
 
{{f5samples
|id=FF:11712-123C2
+
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|name=Mouse Embryonic fibroblasts, donor1
 
|sample_id=11712
 
|rna_tube_id=123C2
 
|rna_box=123
 
|rna_position=C2
 
|sample_cell_lot=N/A
 
|sample_cell_catalog=N/A
 
|sample_company=Sciencell/3H
 
|rna_lot_number=lot:3558
 
|rna_catalog_number=custom
 
|sample_species=Mouse (Mus musculus)
 
|sample_strain=
 
|sample_dev_stage=
 
|sample_tissue=unclassifiable
 
|sample_donor(cell lot)=
 
|sample_sex=
 
|sample_age=
 
|sample_ethnicity=
 
|rna_rin=9.8
 
|rna_od260/230=
 
|rna_od260/280=
 
|sample_cell_type=fibroblast
 
|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-TRIzol-isopropanol-v1.0
 
|rna_weight_ug=10
 
|rna_concentration=1.26
 
|sample_note=
 
|profile_hcage=CNhs12130,LSID839,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
 
|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=
 
|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:11712-123C2
 
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000107
 
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000107
 +
|name=Mouse Embryonic fibroblasts, donor1
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 +
|profile_cagescan=,,,
 +
|profile_hcage=CNhs12130,LSID839,release011,COMPLETED
 +
|profile_rnaseq=,,,
 +
|profile_srnaseq=,,,
 +
|rna_box=123
 +
|rna_catalog_number=custom
 +
|rna_concentration=1.26
 +
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
 +
|rna_lot_number=lot:3558
 +
|rna_od260/230=
 +
|rna_od260/280=
 +
|rna_position=C2
 +
|rna_rin=9.8
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=123C2
 +
|rna_weight_ug=10
 +
|sample_age=
 +
|sample_cell_catalog=N/A
 +
|sample_cell_line=
 +
|sample_cell_lot=N/A
 +
|sample_cell_type=fibroblast
 +
|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=11712
 +
|sample_note=
 +
|sample_sex=
 +
|sample_species=Mouse (Mus musculus)
 +
|sample_strain=
 +
|sample_tissue=unclassifiable
 +
|top_motifs=
 
}}
 
}}

Revision as of 06:00, 21 March 2012


Name:Mouse Embryonic fibroblasts, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexNA
ageNA
cell typefibroblast
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:3558
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} 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

CNhs12130



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: CNhs12130This 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: CNhs12130This 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: CNhs12130


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)

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