Personal tools

FF:11326-117E3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(20 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:11326-117E3
|DRA_sample_Accession=CAGE@SAMD00005194
|name=Fibroblast - Aortic Adventitial, donor2
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005194
|sample_id=11326
|accession_numbers=CAGE;DRX008241;DRR009113;DRZ000538;DRZ001923;DRZ011888;DRZ013273
|rna_tube_id=117E3
|accession_numbers_RNASeq=sRNA-Seq;DRX037173;DRR041539;DRZ007181
|rna_box=117
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000947,UBERON:0001637,UBERON:0000483,UBERON:0002384,UBERON:0000479,UBERON:0000055,UBERON:0000064,UBERON:0000062,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0004923,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0004573,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0002049,UBERON:0004797,UBERON:0010317,UBERON:0007798,UBERON:0000415,UBERON:0007240,UBERON:0005742,UBERON:0005734,UBERON:0004664,UBERON:0004535,UBERON:0004571,UBERON:0010191,UBERON:0004572,UBERON:0004537,UBERON:0001009,UBERON:0004663
|rna_position=E3
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057,CL:1000306,CL:0002547
|sample_cell_lot=lot:7F3048
|sample_cell_catalog=CC-7014
|sample_company=Lonza
|rna_lot_number=
|rna_catalog_number=N/A
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=65 years old adult
|sample_tissue=aorta
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=65
|sample_ethnicity=C
|rna_rin=10
|rna_od260/230=2.04
|rna_od260/280=2.036666667
|sample_cell_type=fibroblast
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=27.24333333
|rna_concentration=1.238
|sample_note=
|profile_hcage=CNhs11968,LSID836,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10011,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371,CL:0002547,CL:1000306
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000055,UBERON:0000060,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000415,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000947,UBERON:0001009,UBERON:0001062,UBERON:0001637,UBERON:0001981,UBERON:0002049,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0003081,UBERON:0003509,UBERON:0003914,UBERON:0004111,UBERON:0004120,UBERON:0004535,UBERON:0004537,UBERON:0004571,UBERON:0004572,UBERON:0004573,UBERON:0004663,UBERON:0004664,UBERON:0004872,UBERON:0004923,UBERON:0005423,UBERON:0005734,UBERON:0005742,UBERON:0006965,UBERON:0007240,UBERON:0007500,UBERON:0007798
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000057,FF:0000001,FF:0000058
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000134
|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=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|is_a=EFO:0002091;;FF:0000002;;FF:0000058;;FF:0000210
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Aortic%2520Adventitial%252c%2520donor2.CNhs11968.11326-117E3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Aortic%2520Adventitial%252c%2520donor2.CNhs11968.11326-117E3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Aortic%2520Adventitial%252c%2520donor2.CNhs11968.11326-117E3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Aortic%2520Adventitial%252c%2520donor2.CNhs11968.11326-117E3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Aortic%2520Adventitial%252c%2520donor2.CNhs11968.11326-117E3.hg38.nobarcode.ctss.bed.gz
|id=FF:11326-117E3
|is_a=EFO:0002091;;FF:0000058
|is_obsolete=
|library_id=CNhs11968
|library_id_phase_based=2:CNhs11968
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11326
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10011.AGTCAA.11326
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11326
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10011.AGTCAA.11326
|name=Fibroblast - Aortic Adventitial, donor2
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11968,LSID836,release011,COMPLETED
|profile_rnaseq=
|profile_srnaseq=SRhi10011,,,
|rna_box=117
|rna_catalog_number=N/A
|rna_concentration=1.238
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.04
|rna_od260/280=2.036666667
|rna_position=E3
|rna_rin=10
|rna_sample_type=total RNA
|rna_tube_id=1.17E+05
|rna_weight_ug=27.24333333
|rnaseq_library_id=SRhi10011.AGTCAA
|sample_age=65
|sample_category=primary cells
|sample_cell_catalog=CC-7014
|sample_cell_line=
|sample_cell_lot=lot:7F3048
|sample_cell_type=fibroblast
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Lonza
|sample_description=
|sample_dev_stage=65 years old adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=11326
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=aorta
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11326-117E3;search_select_hide=table117:FF:11326-117E3
}}
}}

Latest revision as of 17:52, 4 June 2020


Name:Fibroblast - Aortic Adventitial, donor2
Species:Human (Homo sapiens)
Library ID:CNhs11968
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueaorta
dev stage65 years old adult
sexmale
age65
cell typefibroblast
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005194
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11968 CAGE DRX008241 DRR009113
Accession ID Hg19

Library idBAMCTSS
CNhs11968 DRZ000538 DRZ001923
Accession ID Hg38

Library idBAMCTSS
CNhs11968 DRZ011888 DRZ013273
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005194
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10011.AGTCAA sRNA-Seq DRX037173 DRR041539
Accession ID Hg19

Library idBAMCTSS
SRhi10011.AGTCAA DRZ007181





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: CNhs11968This 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: CNhs11968This 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: CNhs11968


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)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
1000306 (fibroblast of tunica adventitia of artery)
0002547 (fibroblast of the aortic adventitia)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000947 (aorta)
0001637 (artery)
0000483 (epithelium)
0002384 (connective tissue)
0000479 (tissue)
0000055 (vessel)
0000064 (organ part)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0004923 (organ component layer)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0004573 (systemic artery)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0002049 (vasculature)
0004797 (blood vessel layer)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0000415 (artery wall)
0007240 (tunica adventitia of artery)
0005742 (adventitia)
0005734 (tunica adventitia of blood vessel)
0004664 (aorta tunica adventitia)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0010191 (aortic system)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)
0004663 (aorta wall)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000057 (fibroblast sample)
0000001 (sample)
0000058 (human fibroblast of the aortic adventitia 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
CL:0000134 (mesenchymal cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11326-117E3&oldid=4576374"