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(Created page with "{{f5samples |id=FF:10094-102C4 |name= |sample_id=10094 |rna_tube_id=102C4 |rna_box=102 |rna_position=C4 |sample_cell_lot=NA |sample_cell_catalog=NA |sample_company=Clontech |r...")
 
 
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{{f5samples
 
{{f5samples
|id=FF:10094-102C4
+
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001134,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002036,UBERON:0002385,UBERON:0010317,UBERON:0001015,UBERON:0002204,UBERON:0000383
|name=
 
|sample_id=10094
 
|rna_tube_id=102C4
 
|rna_box=102
 
|rna_position=C4
 
|sample_cell_lot=NA
 
|sample_cell_catalog=NA
 
|sample_company=Clontech
 
|rna_lot_number=8101369A-14
 
|rna_catalog_number=Cat: 636643 Lot: 8101369A-14
 
|sample_species=Human (Homo sapiens)
 
|sample_strain=
 
|sample_dev_stage=43,46 years old adult
 
|sample_tissue=skeletal muscle
 
|sample_donor(cell lot)=2 pool
 
|sample_sex=mixed
 
|sample_age=
 
|sample_ethnicity=C
 
|rna_rin=
 
|rna_od260/230=
 
|rna_od260/280=
 
|sample_cell_type=CELL MIXTURE - tissue sample
 
|sample_cell_line=
 
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
 
|sample_experimental_condition=
 
|sample_disease=normal
 
|rna_sample_type=total RNA
 
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
 
|rna_weight_ug=10
 
|rna_concentration=1
 
|sample_note=biological replicate
 
|profile_hcage=,,skip,IN_LIBRARIAN
 
|profile_cagescan=
 
|profile_srnaseq=
 
|profile_rnaseq=
 
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000119,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000490,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001015,UBERON:0001062,UBERON:0001134,UBERON:0002036,UBERON:0002050,UBERON:0002204,UBERON:0002329,UBERON:0002385,UBERON:0002532,UBERON:0003059,UBERON:0003077,UBERON:0003082,UBERON:0003104,UBERON:0004120,UBERON:0004290,UBERON:0005291,UBERON:0005423,UBERON:0007023,UBERON:0009142
 
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
|sample_description=
+
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000101,FF:0000001,FF:0000998,FF:0000004,FF:0010023
 +
|comment=
 +
|created_by=
 +
|creation_date=
 +
|def=
 +
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0003104,UBERON:0010316
 
|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=
 +
|has_quality=
 +
|id=FF:10094-102C4
 +
|is_a=EFO:0002091;;FF:0010023
 +
|is_obsolete=
 +
|name=
 +
|namespace=FANTOM5
 +
|part_of=
 +
|profile_cagescan=
 +
|profile_hcage=,,skip,IN_LIBRARIAN
 +
|profile_rnaseq=
 +
|profile_srnaseq=
 +
|rna_box=102
 +
|rna_catalog_number=Cat: 636643 Lot: 8101369A-14
 +
|rna_concentration=1
 +
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
 +
|rna_lot_number=8101369A-14
 +
|rna_od260/230=
 +
|rna_od260/280=
 +
|rna_position=C4
 +
|rna_rin=
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=102C4
 +
|rna_weight_ug=10
 +
|sample_age=
 +
|sample_cell_catalog=NA
 +
|sample_cell_line=
 +
|sample_cell_lot=NA
 +
|sample_cell_type=CELL MIXTURE - tissue sample
 +
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
 +
|sample_company=Clontech
 +
|sample_description=
 +
|sample_dev_stage=43,46 years old adult
 +
|sample_disease=normal
 +
|sample_donor(cell lot)=2 pool
 +
|sample_ethnicity=C
 +
|sample_experimental_condition=
 +
|sample_id=10094
 +
|sample_note=biological replicate
 +
|sample_sex=mixed
 +
|sample_species=Human (Homo sapiens)
 +
|sample_strain=
 +
|sample_tissue=skeletal muscle
 
|top_motifs=
 
|top_motifs=
 +
|xref=
 
}}
 
}}

Latest revision as of 09:15, 9 July 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
tissueskeletal muscle
dev stage43,46 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8101369A-14
catalog numberCat: 636643 Lot: 8101369A-14
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.
Analyst:NA

link to dataset.
data


Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0001134 (skeletal muscle tissue)
0000479 (tissue)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0010317 (germ layer / neural crest derived structure)
0001015 (musculature)
0002204 (musculoskeletal system)
0000383 (musculature of body)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010023 (human skeletal muscle - adult sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0003104 (mesenchyme)
UBERON:0010316 (germ layer / neural crest)