Personal tools

FF:11287-116I9: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005652
|DRA_sample_Accession=CAGE@SAMD00005652
|accession_numbers=CAGE;DRX008491;DRR009363;DRZ000788;DRZ002173
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005652
|accession_numbers=CAGE;DRX008491;DRR009363;DRZ000788;DRZ002173;DRZ012138;DRZ013523
|accession_numbers_RNASeq=sRNA-Seq;DRX037260;DRR041626;DRZ007268
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001637,UBERON:0002100,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0009569,UBERON:0004573,UBERON:0003834,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0002049,UBERON:0003513,UBERON:0010317,UBERON:0007798,UBERON:0002456,UBERON:0001533,UBERON:0004535,UBERON:0004571,UBERON:0000915,UBERON:0004572,UBERON:0004537,UBERON:0001009
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001637,UBERON:0002100,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0009569,UBERON:0004573,UBERON:0003834,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0002049,UBERON:0003513,UBERON:0010317,UBERON:0007798,UBERON:0002456,UBERON:0001533,UBERON:0004535,UBERON:0004571,UBERON:0000915,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:0002595,CL:0002593
|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:0002595,CL:0002593
Line 40: Line 42:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Internal%2520Thoracic%2520Artery%252c%2520donor1.CNhs11067.11287-116I9.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Internal%2520Thoracic%2520Artery%252c%2520donor1.CNhs11067.11287-116I9.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Internal%2520Thoracic%2520Artery%252c%2520donor1.CNhs11067.11287-116I9.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Internal%2520Thoracic%2520Artery%252c%2520donor1.CNhs11067.11287-116I9.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Internal%2520Thoracic%2520Artery%252c%2520donor1.CNhs11067.11287-116I9.hg38.nobarcode.ctss.bed.gz
|id=FF:11287-116I9
|id=FF:11287-116I9
|is_a=EFO:0002091;;FF:0000173
|is_a=EFO:0002091;;FF:0000173
Line 45: Line 52:
|library_id=CNhs11067
|library_id=CNhs11067
|library_id_phase_based=2:CNhs11067
|library_id_phase_based=2:CNhs11067
|name="Smooth Muscle Cells - Internal Thoracic Artery, donor1"
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11287
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10015.GTAGAG.11287
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11287
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10015.GTAGAG.11287
|name=Smooth Muscle Cells - Internal Thoracic Artery, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage="CNhs11067,LSID723,release008,COMPLETED"
|profile_hcage=CNhs11067,LSID723,release008,COMPLETED
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq="SRhi10015,,,"
|profile_srnaseq=SRhi10015,,,
|rna_box=116
|rna_box=116
|rna_catalog_number=CA358-R10a
|rna_catalog_number=CA358-R10a
Line 64: Line 77:
|rna_tube_id=116I9
|rna_tube_id=116I9
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=SRhi10015.GTAGAG
|sample_age=34
|sample_age=34
|sample_category=primary cells
|sample_category=primary cells
Line 86: Line 100:
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11287-116I9;search_select_hide=table117:FF:11287-116I9
}}
}}

Latest revision as of 16:31, 3 June 2020


Name:Smooth Muscle Cells - Internal Thoracic Artery, donor1
Species:Human (Homo sapiens)
Library ID:CNhs11067
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueinternal thoracic artery
dev stage34 years old adult
sexfemale
age34
cell typesmooth muscle cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1696
catalog numberCA358-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005652
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11067 CAGE DRX008491 DRR009363
Accession ID Hg19

Library idBAMCTSS
CNhs11067 DRZ000788 DRZ002173
Accession ID Hg38

Library idBAMCTSS
CNhs11067 DRZ012138 DRZ013523
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005652
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10015.GTAGAG sRNA-Seq DRX037260 DRR041626
Accession ID Hg19

Library idBAMCTSS
SRhi10015.GTAGAG DRZ007268





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: CNhs11067This 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: CNhs11067This 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: CNhs11067


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)
0002595 (smooth muscle cell of the subclavian artery)
0002593 (smooth muscle cell of the internal thoracic artery)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001637 (artery)
0002100 (trunk)
0000483 (epithelium)
0000479 (tissue)
0000055 (vessel)
0004111 (anatomical conduit)
0000475 (organism subdivision)
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)
0009569 (subdivision of trunk)
0004573 (systemic artery)
0003834 (thoracic segment blood vessel)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0002049 (vasculature)
0003513 (trunk blood vessel)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0002456 (internal thoracic artery)
0001533 (subclavian artery)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0000915 (thoracic segment of trunk)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000167 (smooth muscle cell sample)
0000173 (human smooth muscle cell of the internal thoracic artery 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:11287-116I9&oldid=4576341"