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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005115
|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005115!sRNA-Seq@SAMD00005115
|accession_numbers=CAGE;DRX008500;DRR009372;DRZ000797;DRZ002182;DRZ012147;DRZ013532
|accession_numbers_RNASeq=RNA-Seq;DRX057111;DRR062870;DRZ007946!sRNA-Seq;DRX037171;DRR041537;DRZ007179
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004121,UBERON:0004119,UBERON:0010314,UBERON:0004111,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0005911,UBERON:0000477,UBERON:0000467,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0010371,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0000078,UBERON:0002049,UBERON:0010317,UBERON:0007798,UBERON:0002012,UBERON:0004535,UBERON:0004572,UBERON:0004537,UBERON:0008886,UBERON:0001009
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004121,UBERON:0004119,UBERON:0010314,UBERON:0004111,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0005911,UBERON:0000477,UBERON:0000467,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0010371,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0000078,UBERON:0002049,UBERON:0010317,UBERON:0007798,UBERON:0002012,UBERON:0004535,UBERON:0004572,UBERON:0004537,UBERON:0008886,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:0002591
|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:0002591
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|created_by=
|created_by=
|creation_date=
|creation_date=
|datafreeze_phase=1
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|ffid_belonging_in_development=CL:0000355,CL:0000222,CL:0000514
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
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|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-%2520Pulmonary%2520Artery%252c%2520donor3.CNhs12047.11437-118H6.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Pulmonary%2520Artery%252c%2520donor3.CNhs12047.11437-118H6.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Pulmonary%2520Artery%252c%2520donor3.CNhs12047.11437-118H6.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-%2520Pulmonary%2520Artery%252c%2520donor3.CNhs12047.11437-118H6.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Pulmonary%2520Artery%252c%2520donor3.CNhs12047.11437-118H6.hg38.nobarcode.ctss.bed.gz
|id=FF:11437-118H6
|id=FF:11437-118H6
|is_a=EFO:0002091;;FF:0000174
|is_a=EFO:0002091;;FF:0000174
|is_obsolete=
|is_obsolete=
|library_id=CNhs12047
|library_id_phase_based=2:CNhs12047
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11437
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10011.TAGCTT.11437
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11437
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10011.TAGCTT.11437
|name=Smooth Muscle Cells - Pulmonary Artery, donor3
|name=Smooth Muscle Cells - Pulmonary Artery, donor3
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs12047,LSID838,release011,COMPLETED
|profile_hcage=CNhs12047,LSID838,release011,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=SRhi10011,,,
|profile_srnaseq=SRhi10011,,,
|rna_box=118
|rna_box=118
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|rna_tube_id=118H6
|rna_tube_id=118H6
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=RDhi10053!SRhi10011.TAGCTT
|sample_age=42
|sample_age=42
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_line=
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|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11437-118H6;search_select_hide=table117:FF:11437-118H6
}}
}}

Latest revision as of 18:01, 4 June 2020


Name:Smooth Muscle Cells - Pulmonary Artery, donor3
Species:Human (Homo sapiens)
Library ID:CNhs12047
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuepulmonary artery
dev stage42 years old adult
sexfemale
age42
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 number1055
catalog numberCA352-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005115
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12047 CAGE DRX008500 DRR009372
Accession ID Hg19

Library idBAMCTSS
CNhs12047 DRZ000797 DRZ002182
Accession ID Hg38

Library idBAMCTSS
CNhs12047 DRZ012147 DRZ013532
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
RNA-Seq  SAMD00005115
sRNA-Seq  SAMD00005115
Library accession numbers

Library idMethodExp. accession idRun accession id
RDhi10053 RNA-Seq DRX057111 DRR062870
SRhi10011.TAGCTT sRNA-Seq DRX037171 DRR041537
Accession ID Hg19

Library idBAMCTSS
RDhi10053 DRZ007946
SRhi10011.TAGCTT DRZ007179





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: CNhs12047This 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: CNhs12047This 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: CNhs12047


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)
0002591 (smooth muscle cell of the pulmonary artery)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001637 (artery)
0000483 (epithelium)
0000479 (tissue)
0000055 (vessel)
0004121 (ectoderm-derived structure)
0004119 (endoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0005911 (endo-epithelium)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0010371 (ecto-epithelium)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0002049 (vasculature)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0002012 (pulmonary artery)
0004535 (cardiovascular system)
0004572 (arterial system)
0004537 (blood vasculature)
0008886 (pulmonary vascular system)
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)
0000174 (human smooth muscle cell of pulmonary 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)

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