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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004889
|DRA_sample_Accession=CAGE@SAMD00004889
|accession_numbers=CAGE;DRX008344;DRR009216;DRZ000641;DRZ002026
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00004889
|accession_numbers=CAGE;DRX008344;DRR009216;DRZ000641;DRZ002026;DRZ011991;DRZ013376
|accession_numbers_RNASeq=sRNA-Seq;DRX037074;DRR041440;DRZ007082
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000075,UBERON:0004765,UBERON:0002513,UBERON:0008001,UBERON:0010913,UBERON:0010363,UBERON:0002412,UBERON:0002204,UBERON:0001434,UBERON:0011138,UBERON:0001130
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000075,UBERON:0004765,UBERON:0002513,UBERON:0008001,UBERON:0010913,UBERON:0010363,UBERON:0002412,UBERON:0002204,UBERON:0001434,UBERON:0011138,UBERON:0001130
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000255,CL:0000034,CL:0002572
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000255,CL:0000034,CL:0002572
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|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=1
|data_phase=2
|datafreeze_phase=1
|datafreeze_phase=2
|def=
|def=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000034;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000134;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0000075;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0007844
|ffid_belonging_in_development=CL:0000134
|ffid_belonging_in_development=CL:0000134
|fonse_cell_line=
|fonse_cell_line=
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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/Mesenchymal%2520Stem%2520Cells%2520-%2520Vertebral%252c%2520donor1.CNhs10846.11219-116B4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Mesenchymal%2520Stem%2520Cells%2520-%2520Vertebral%252c%2520donor1.CNhs10846.11219-116B4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Mesenchymal%2520Stem%2520Cells%2520-%2520Vertebral%252c%2520donor1.CNhs10846.11219-116B4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Mesenchymal%2520Stem%2520Cells%2520-%2520Vertebral%252c%2520donor1.CNhs10846.11219-116B4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Mesenchymal%2520Stem%2520Cells%2520-%2520Vertebral%252c%2520donor1.CNhs10846.11219-116B4.hg38.nobarcode.ctss.bed.gz
|id=FF:11219-116B4
|id=FF:11219-116B4
|is_a=EFO:0002091;;FF:0000093
|is_a=EFO:0002091;;FF:0000093
|is_obsolete=
|is_obsolete=
|library_id=CNhs10846
|library_id=CNhs10846
|library_id_phase_based=1:CNhs10846
|library_id_phase_based=2:CNhs10846
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11219
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10006.CAGATC.11219
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11219
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10006.CAGATC.11219
|name=Mesenchymal Stem Cells - Vertebral, donor1
|name=Mesenchymal Stem Cells - Vertebral, donor1
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs10846,LSID700,release009,COMPLETED
|profile_hcage=CNhs10846,LSID700,release009,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=SRhi10006,,,
|profile_srnaseq=SRhi10006,,,
|rna_box=116
|rna_box=116
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|rna_tube_id=116B4
|rna_tube_id=116B4
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=SRhi10006.CAGATC
|sample_age=
|sample_age=
|sample_category=primary cells
|sample_category=primary cells
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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:11219-116B4;search_select_hide=table117:FF:11219-116B4
}}
}}

Latest revision as of 16:25, 3 June 2020

Name:Mesenchymal Stem Cells - Vertebral, donor1
Species:Human (Homo sapiens)
Library ID:CNhs10846
Sample type:primary cells
Genomic View: UCSC
FANTOM CAT:1, 2, 3, 4
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuespinal cord
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC7555
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004889
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10846 CAGE DRX008344 DRR009216
Accession ID Hg19

Library idBAMCTSS
CNhs10846 DRZ000641 DRZ002026
Accession ID Hg38

Library idBAMCTSS
CNhs10846 DRZ011991 DRZ013376
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00004889
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10006.CAGATC sRNA-Seq DRX037074 DRR041440
Accession ID Hg19

Library idBAMCTSS
SRhi10006.CAGATC DRZ007082





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: CNhs10846This 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: CNhs10846This 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: CNhs10846


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002572 (vertebral mesenchymal stem cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0002513 (endochondral bone)
0008001 (irregular bone)
0010913 (vertebral element)
0010363 (endochondral element)
0002412 (vertebra)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0011138 (post-cranial axial skeletal system)
0001130 (vertebral column)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000093 (human vertebral mesenchymal stem cell 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)

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