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{{f5samples
{{f5samples
|id=FF:10319-105A4
|DRA_sample_Accession=CAGE@SAMD00006005
|name=Urethra, donor2
|accession_numbers=CAGE;DRX008613;DRR009485;DRZ000910;DRZ002295;DRZ012260;DRZ013645
|sample_id=10319
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000057,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0004111,UBERON:0004120,UBERON:0000077,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001556,UBERON:0001008
|rna_tube_id=105A4
|rna_box=105
|rna_position=A4
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=2-Ut
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=Urethra
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=4.1
|rna_od260/230=1.81
|rna_od260/280=2.08
|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=14.69475
|rna_concentration=0.54425
|sample_note=
|profile_hcage=CNhs13464,LSID1024,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000057,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001008,UBERON:0001046,UBERON:0001062,UBERON:0001353,UBERON:0001555,UBERON:0001556,UBERON:0002050,UBERON:0002532,UBERON:0003064,UBERON:0003104,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0006554,UBERON:0006866,UBERON:0007023,UBERON:0007026,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:0011181
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|f5samples=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0000161;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001008;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001353;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001556;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0004122
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0010316
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 41:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/Urethra%252c%2520donor2.CNhs13464.10319-105A4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/Urethra%252c%2520donor2.CNhs13464.10319-105A4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/Urethra%252c%2520donor2.CNhs13464.10319-105A4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/Urethra%252c%2520donor2.CNhs13464.10319-105A4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/Urethra%252c%2520donor2.CNhs13464.10319-105A4.hg38.nobarcode.ctss.bed.gz
|id=FF:10319-105A4
|is_a=EFO:0002091;;FF:0011181
|is_obsolete=
|library_id=CNhs13464
|library_id_phase_based=2:CNhs13464
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10319
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10319
|name=Urethra, donor2
|namespace=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13464,LSID1024,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=105
|rna_catalog_number=
|rna_concentration=0.54425
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=2-Ut
|rna_od260/230=1.81
|rna_od260/280=2.08
|rna_position=A4
|rna_rin=4.1
|rna_sample_type=total RNA
|rna_tube_id=105A4
|rna_weight_ug=14.69475
|sample_age=
|sample_category=tissues
|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=10319
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=Urethra
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10319-105A4;search_select_hide=table117:FF:10319-105A4
}}
}}

Latest revision as of 13:58, 3 June 2020

Name:Urethra, donor2
Species:Human (Homo sapiens)
Library ID:CNhs13464
Sample type:tissues
Genomic View: UCSC
FANTOM CAT:1, 2, 3, 4, 5
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueUrethra
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 number2-Ut
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00006005
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13464 CAGE DRX008613 DRR009485
Accession ID Hg19

Library idBAMCTSS
CNhs13464 DRZ000910 DRZ002295
Accession ID Hg38

Library idBAMCTSS
CNhs13464 DRZ012260 DRZ013645
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload





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>dataNo results for this sample

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
library id: CNhs13464This sample isn't target for the analysis

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
library id: CNhs13464This sample isn't target for the analysis

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> library id: CNhs13464


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)
0000057 (urethra)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001556 (lower urinary tract)
0001008 (renal system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011181 (human Urethra 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:0010316 (germ layer / neural crest)

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