Personal tools

FF:12757-136B3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021495
|accession_numbers=CAGE;DRX023150;DRR025489;DRZ003914;DRZ004797;DRZ008655;DRZ009538
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001135,UBERON:0000947,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0004573,UBERON:0002385,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0004237,UBERON:0004695,UBERON:0002049,UBERON:0010317,UBERON:0002111,UBERON:0007798,UBERON:0001015,UBERON:0004178,UBERON:0002204,UBERON:0004535,UBERON:0004571,UBERON:0010191,UBERON:0000383,UBERON:0004572,UBERON:0004537,UBERON:0001009
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001135,UBERON:0000947,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0004573,UBERON:0002385,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0004237,UBERON:0004695,UBERON:0002049,UBERON:0010317,UBERON:0002111,UBERON:0007798,UBERON:0001015,UBERON:0004178,UBERON:0002204,UBERON:0004535,UBERON:0004571,UBERON:0010191,UBERON:0000383,UBERON:0004572,UBERON:0004537,UBERON:0001009
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000255,CL:0000359,CL:0002539
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000255,CL:0000359,CL:0002539
Line 7: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|donor=biol_rep2 (LK53)
|ffid_belonging_in_development=CL:0000355,CL:0000222,CL:0000514
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 35: Line 41:
|fonse_treatment_closure=EFO:0000369,FF:0000340,FF:0000563,FF:12757-136B3
|fonse_treatment_closure=EFO:0000369,FF:0000340,FF:0000563,FF:12757-136B3
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Aortic%2520smooth%2520muscle%2520cell%2520response%2520to%2520IL1b%252c%252004hr%252c%2520biol_rep2%2520%2528LK53%2529.CNhs13376.12757-136B3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Aortic%2520smooth%2520muscle%2520cell%2520response%2520to%2520IL1b%252c%252004hr%252c%2520biol_rep2%2520%2528LK53%2529.CNhs13376.12757-136B3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Aortic%2520smooth%2520muscle%2520cell%2520response%2520to%2520IL1b%252c%252004hr%252c%2520biol_rep2%2520%2528LK53%2529.CNhs13376.12757-136B3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Aortic%2520smooth%2520muscle%2520cell%2520response%2520to%2520IL1b%252c%252004hr%252c%2520biol_rep2%2520%2528LK53%2529.CNhs13376.12757-136B3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Aortic%2520smooth%2520muscle%2520cell%2520response%2520to%2520IL1b%252c%252004hr%252c%2520biol_rep2%2520%2528LK53%2529.CNhs13376.12757-136B3.hg38.nobarcode.ctss.bed.gz
|id=FF:12757-136B3
|id=FF:12757-136B3
|is_a=EFO:0002091;;FF:0000563
|is_a=EFO:0002091;;FF:0000563
|is_obsolete=
|is_obsolete=
|name=Aortic smooth muscle cell response to IL1b, 04hr, biol_rep2 (LK53)
|library_id=CNhs13376
|library_id_phase_based=2:CNhs13376
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12757
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12757
|name=Aortic smooth muscle cell response to IL1b
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs13376,LSID1022,release013,COMPLETED
|profile_hcage=CNhs13376,LSID1022,release013,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|rna_box=136
|rna_box=136
Line 58: Line 75:
|rna_weight_ug=5.62
|rna_weight_ug=5.62
|sample_age=
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_line=
Line 76: Line 94:
|sample_strain=
|sample_strain=
|sample_tissue=aorta
|sample_tissue=aorta
|time= 04hr
|timecourse=AoSMC_response_to_IL1b
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12757-136B3;search_select_hide=table117:FF:12757-136B3
}}
}}

Latest revision as of 18:44, 4 June 2020


Name:Aortic smooth muscle cell response to IL1b
Species:Human (Homo sapiens)
Library ID:CNhs13376
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueaorta
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell, vascular associated
cell lineNA
companyNA
collaborationLevon Khachigian (University of New South Wales)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021495
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13376 CAGE DRX023150 DRR025489
Accession ID Hg19

Library idBAMCTSS
CNhs13376 DRZ003914 DRZ004797
Accession ID Hg38

Library idBAMCTSS
CNhs13376 DRZ008655 DRZ009538
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: CNhs13376This 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: CNhs13376This 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: CNhs13376


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)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0000359 (vascular associated smooth muscle cell)
0002539 (aortic smooth muscle cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001135 (smooth muscle tissue)
0000947 (aorta)
0001637 (artery)
0000483 (epithelium)
0000479 (tissue)
0000055 (vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0004573 (systemic artery)
0002385 (muscle tissue)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0004237 (blood vessel smooth muscle)
0004695 (arterial system smooth muscle)
0002049 (vasculature)
0010317 (germ layer / neural crest derived structure)
0002111 (artery smooth muscle tissue)
0007798 (vascular system)
0001015 (musculature)
0004178 (aorta smooth muscle tissue)
0002204 (musculoskeletal system)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0010191 (aortic system)
0000383 (musculature of body)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)

FF: FANTOM5
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000350 (experimentally modified sample)
0000361 (4 hr sample)
0000340 (IL1-beta treatment sample)
0000563 (human Aortic Smooth Muscle cells 4hr after treatment with IL1b 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:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)
CL:0000514 (smooth muscle myoblast)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:12757-136B3&oldid=4577258"