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{{f5samples
{{f5samples
|id=FF:10095-102C5
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0002106,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002323,UBERON:0005177,UBERON:0004177,UBERON:0005057,UBERON:0005172,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0005173,UBERON:0002390,UBERON:0002417,UBERON:0002193,UBERON:0000916,UBERON:0002405
|name=
|sample_id=10095
|rna_tube_id=102C5
|rna_box=102
|rna_position=C5
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Clontech
|rna_lot_number=8101369A-15
|rna_catalog_number=Cat: 636643 Lot: 8101369A-15
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=18-54 years old adult
|sample_tissue=spleen
|sample_donor(cell lot)=12 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:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002095,UBERON:0002100,UBERON:0002106,UBERON:0002193,UBERON:0002323,UBERON:0002390,UBERON:0002405,UBERON:0002417,UBERON:0002532,UBERON:0002553,UBERON:0003081,UBERON:0003104,UBERON:0003281,UBERON:0004119,UBERON:0004120,UBERON:0004177,UBERON:0004185,UBERON:0004457,UBERON:0004458,UBERON:0004782,UBERON:0004854,UBERON:0004872,UBERON:0004921,UBERON:0004923,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0005602,UBERON:0006293,UBERON:0007023,UBERON:0007026,UBERON:0009034,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:0010025
|comment=
|created_by=
|creation_date=
|def=
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0004872,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:10095-102C5
|is_a=EFO:0002091;;FF:0010025
|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-15
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=8101369A-15
|rna_od260/230=
|rna_od260/280=
|rna_position=C5
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=102C5
|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=18-54 years old adult
|sample_disease=normal
|sample_donor(cell lot)=12 pool
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10095
|sample_note=biological replicate
|sample_sex=mixed
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=spleen
|top_motifs=
|top_motifs=
|xref=
}}
}}

Latest revision as of 18:15, 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
tissuespleen
dev stage18-54 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-15
catalog numberCat: 636643 Lot: 8101369A-15
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. <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)
0002106 (spleen)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002323 (body cavity)
0005177 (trunk region element)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010025 (human spleen - adult sample)

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:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)

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