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{{f5samples
{{f5samples
|id=FF:11832-124G5
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000025,UBERON:0000055,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000119,UBERON:0000353,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001009,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001280,UBERON:0001281,UBERON:0001555,UBERON:0001981,UBERON:0002049,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003081,UBERON:0003104,UBERON:0003497,UBERON:0003513,UBERON:0003835,UBERON:0003894,UBERON:0003909,UBERON:0003914,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004535,UBERON:0004537,UBERON:0004647,UBERON:0004872,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0006235,UBERON:0006925,UBERON:0006965,UBERON:0007026,UBERON:0007500,UBERON:0007798,UBERON:0008835,UBERON:0008836,UBERON:0009142
|name=
|sample_id=11832
|rna_tube_id=124G5
|rna_box=124
|rna_position=G5
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=
|sample_tissue=liver
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=2.02
|sample_cell_type=hepatic sinusoidal endothelial cell
|sample_cell_line=
|sample_collaboration=Soichi Kojima (RIKEN ASI)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=1.4545
|rna_concentration=0.05818
|sample_note=
|profile_hcage=,,,SKIP_ADDITIONAL
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000115,CL:0000144,CL:0000213,CL:0000215,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0002078,CL:0002262,CL:0002321,CL:0002371,CL:1000398
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000115,CL:0000144,CL:0000213,CL:0000215,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0002078,CL:0002262,CL:0002321,CL:0002371,CL:1000398
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000025,UBERON:0000055,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000119,UBERON:0000353,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001009,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001280,UBERON:0001281,UBERON:0001555,UBERON:0001981,UBERON:0002049,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003081,UBERON:0003104,UBERON:0003497,UBERON:0003513,UBERON:0003835,UBERON:0003894,UBERON:0003909,UBERON:0003914,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004535,UBERON:0004537,UBERON:0004647,UBERON:0004872,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0006235,UBERON:0006925,UBERON:0006965,UBERON:0007026,UBERON:0007500,UBERON:0007798,UBERON:0008835,UBERON:0008836,UBERON:0009142
|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=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11832-124G5
|is_a=EFO:0002091;;FF:0011161
|is_a=EFO:0002091;;FF:0011161
|name=
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=,,,SKIP_ADDITIONAL
|profile_rnaseq=
|profile_srnaseq=
|rna_box=124
|rna_catalog_number=
|rna_concentration=0.05818
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=2.02
|rna_position=G5
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=124G5
|rna_weight_ug=1.4545
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=hepatic sinusoidal endothelial cell
|sample_collaboration=Soichi Kojima (RIKEN ASI)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11832
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=liver
|top_motifs=
}}
}}

Revision as of 15:03, 21 March 2012


Name:
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stageNA
sexmale
ageNA
cell typehepatic sinusoidal endothelial cell
cell lineNA
companyNA
collaborationSoichi Kojima (RIKEN ASI)
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
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

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)
0000066 (epithelial cell)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002262 (endothelial cell of sinusoid)
0002321 (embryonic cell)
0002371 (somatic cell)
1000398 (endothelial cell of hepatic sinusoid)

UBERON: Anatomy
0000015 (anatomical boundary)
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000353 (parenchyma)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001009 (circulatory system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001280 (liver parenchyma)
0001281 (hepatic sinusoid)
0001555 (digestive tract)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003497 (abdomen blood vessel)
0003513 (trunk blood vessel)
0003835 (abdominal segment blood vessel)
0003894 (liver primordium)
0003909 (sinusoid)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004647 (liver lobule)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0006965 (vascular cord)
0007026 (primitive gut)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

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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