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{{f5samples
{{f5samples
|id=FF:10285-104F6
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000014,UBERON:0002097,UBERON:0002199,UBERON:0001513,UBERON:0000479,UBERON:0000064,UBERON:0000062,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0008784,UBERON:0001062,UBERON:0000480,UBERON:0003102,UBERON:0003532,UBERON:0004708,UBERON:0002101,UBERON:0004709,UBERON:0002470,UBERON:0002529,UBERON:0010538,UBERON:0001419,UBERON:0010317,UBERON:0010758,UBERON:0010707,UBERON:0002103,UBERON:0002387,UBERON:0000154,UBERON:0010709,UBERON:0002416
|name=Skin - cornified area on sole of foot, donor1
|sample_id=10285
|rna_tube_id=
|rna_box=104
|rna_position=F6
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=1-Sk5
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=Skin - cornified area on sole of foot
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=2.40000
|rna_od260/230=1.64000
|rna_od260/280=2.08000
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Alessandro Bonetti
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=25.22232
|rna_concentration=
|sample_note=
|profile_hcage=,LSID1024,,SEQUENCING QUEUE
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000026,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000154,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001048,UBERON:0001062,UBERON:0001419,UBERON:0001513,UBERON:0002050,UBERON:0002097,UBERON:0002101,UBERON:0002103,UBERON:0002199,UBERON:0002387,UBERON:0002416,UBERON:0002470,UBERON:0002529,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003532,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004709,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0007023,UBERON:0008784
|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:0011176
 
|comment=
|created_by=
|creation_date=
|def=
|f5samples=
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 36:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|id=FF:10285-104F6
|is_a=EFO:0002091;;FF:0011176
|is_obsolete=
|name=
|namespace=
|part_of=
|profile_cagescan=,,,
|profile_hcage=,LSID1024,,SEQUENCING QUEUE
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=104
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=1-Sk5
|rna_od260/230=1.64000
|rna_od260/280=2.08000
|rna_position=F6
|rna_rin=2.40000
|rna_sample_type=total RNA
|rna_tube_id=
|rna_weight_ug=25.22232
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Alessandro Bonetti
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10285
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=Skin - cornified area on sole of foot
|top_motifs=
|xref=
}}
}}

Latest revision as of 15:46, 11 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
tissueSkin - cornified area on sole of foot
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Sk5
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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000014 (zone of skin)
0002097 (skin of body)
0002199 (integument)
0001513 (skin of foot)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0008784 (lower limb segment)
0001062 (anatomical entity)
0000480 (anatomical group)
0003102 (surface structure)
0003532 (hindlimb skin)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0002470 (autopod region)
0002529 (limb segment)
0010538 (paired limb/fin segment)
0001419 (skin of limb)
0010317 (germ layer / neural crest derived structure)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0002103 (hindlimb)
0002387 (foot)
0000154 (posterior region of body)
0010709 (pelvic complex)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011176 (Skin - cornified area on sole of foot)

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

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