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{{f5samples
{{f5samples
|id=FF:10446-106F5
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002048,UBERON:0002100,UBERON:0002384,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915
|name=
|ancestors_in_cell_lineage_facet=CL:0000010,CL:0000000,CL:0000578,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0001034,CL:0000057,CL:0000001,CL:0002553
|sample_id=10446
|rna_tube_id=106F5
|rna_box=106
|rna_position=F5
|sample_cell_lot=
|sample_cell_catalog=RCB0702
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=3 month old child
|sample_tissue=ANATOMICAL SYSTEM
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=fetal 3 month
|sample_ethnicity=unknown
|rna_rin=
|rna_od260/230=1.91
|rna_od260/280=2.12
|sample_cell_type=fibroblast
|sample_cell_line=WI-38
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=28.74725
|rna_concentration=1.14989
|sample_note=
|profile_hcage=,,,IN_LIBRARIAN
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000001,CL:0000003,CL:0000004,CL:0000010,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000578,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002384,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0100353,FF:0100453,FF:0100161,FF:0101958,FF:0100669,FF:0100458
|comment=
|created_by=
|creation_date=
|def=
|f5samples=
|ffid_belonging_in_development=CL:0000134,UBERON:0001041,UBERON:0008947,UBERON:0002532,UBERON:0006595,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=PATO:0000461
|id=FF:10446-106F5
|is_a=CL:0000001;;EFO:0002091;;FF:0000210;;FF:0100458
|is_obsolete=
|name=
|namespace=FANTOM5
|part_of=
|profile_cagescan=
|profile_hcage=,,,IN_LIBRARIAN
|profile_rnaseq=
|profile_srnaseq=
|rna_box=106
|rna_catalog_number=
|rna_concentration=1.14989
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.91
|rna_od260/280=2.12
|rna_position=F5
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=106F5
|rna_weight_ug=28.74725
|sample_age=fetal 3 month
|sample_cell_catalog=RCB0702
|sample_cell_line=WI-38
|sample_cell_lot=
|sample_cell_type=fibroblast
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=3 month old child
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=unknown
|sample_experimental_condition=
|sample_id=10446
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=ANATOMICAL SYSTEM
|top_motifs=
|top_motifs=
|xref=
}}
}}

Latest revision as of 19:01, 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
tissueANATOMICAL SYSTEM
dev stage3 month old child
sexfemale
agefetal 3 month
cell typefibroblast
cell lineWI-38
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

has_quality relathionship
PATO:0000461

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
0000010 (cell culture cell;;obsolete_cell line cell)
0000000 (cell), 0000000 (cell)
0000578 (experimentally modified cell in vitro)
0000003 (native cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0001034 (cell in vitro)
0000057 (fibroblast)
0000001 (primary cell culture cell)
0002553 (lung fibroblast)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002048 (lung)
0002100 (trunk)
0002384 (connective tissue)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100353 (lung cell line sample)
0100453 (fibroblast cell line sample)
0100161 (lung fibroblast cell line sample)
0101958 (embryonic fibroblast cell line)
0100669 (embryonic cell line sample)
0100458 (WI-38 cell)

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
CL:0000134 (mesenchymal cell)
UBERON:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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