Personal tools

FF:11619-122A8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004932
|DRA_sample_Accession=CAGE@SAMD00004932
|accession_numbers=CAGE;DRX008358;DRR009230;DRZ000655;DRZ002040
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00004932
|accession_numbers=CAGE;DRX008358;DRR009230;DRZ000655;DRZ002040;DRZ012005;DRZ013390
|accession_numbers_RNASeq=sRNA-Seq;DRX037080;DRR041446;DRZ007088
|ancestors_in_anatomy_facet=UBERON:0002331,UBERON:0002384,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0001062,UBERON:0000478,UBERON:0003104,UBERON:0010317,UBERON:0003422,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0002331,UBERON:0002384,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0001062,UBERON:0000478,UBERON:0003104,UBERON:0010317,UBERON:0003422,UBERON:0009142
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000349,CL:0000255,CL:0000034,CL:0002569
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000349,CL:0000255,CL:0000034,CL:0002569
Line 53: Line 55:
|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#cage;sample;11619
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11619
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10006.ATGTCA.11619
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10006.ATGTCA.11619
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#cage;sample;11619
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11619
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10006.ATGTCA.11619
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10006.ATGTCA.11619
|name=Mesenchymal Stem Cells - umbilical, donor2
|name=Mesenchymal Stem Cells - umbilical, donor2
Line 76: Line 78:
|rna_tube_id=122A8
|rna_tube_id=122A8
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=SRhi10006.ATGTCA
|sample_age=
|sample_age=
|sample_category=primary cells
|sample_category=primary cells
Line 98: Line 101:
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11619-122A8;search_select_hide=table117:FF:11619-122A8
}}
}}

Latest revision as of 18:12, 4 June 2020

Name:Mesenchymal Stem Cells - umbilical, donor2
Species:Human (Homo sapiens)
Library ID:CNhs12102
Sample type:primary cells
Genomic View: UCSC
FANTOM CAT:1, 2, 3, 4, 5
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueumbilical cord
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC7535
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004932
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12102 CAGE DRX008358 DRR009230
Accession ID Hg19

Library idBAMCTSS
CNhs12102 DRZ000655 DRZ002040
Accession ID Hg38

Library idBAMCTSS
CNhs12102 DRZ012005 DRZ013390
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00004932
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10006.ATGTCA sRNA-Seq DRX037080 DRR041446
Accession ID Hg19

Library idBAMCTSS
SRhi10006.ATGTCA DRZ007088





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: CNhs12102This 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: CNhs12102This 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: CNhs12102


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)
0000349 (extraembryonic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002569 (mesenchymal stem cell of umbilical cord)

UBERON: Anatomy
0002331 (umbilical cord)
0002384 (connective tissue)
0000479 (tissue)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0001062 (anatomical entity)
0000478 (extraembryonic structure)
0003104 (mesenchyme)
0010317 (germ layer / neural crest derived structure)
0003422 (mesenchyme of umbilical cord)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000094 (human mesenchymal stem cell of umbilical cord-Sciencell sample)
0000001 (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:11619-122A8&oldid=4576608"