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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021375
|accession_numbers=CAGE;DRX023903;DRR026302;DRZ005554;DRZ006340;DRZ010169;DRZ010833
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000219,CL:0000004,CL:0000134,CL:0000255
|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
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000346,FF:0000404,FF:0000336,FF:0000474
|comment=
|comment=
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|donor= biol_rep3 (030mB3)
|ffid_belonging_in_development=CL:0000134
|fonse_cell_line=FF:0000404
|fonse_cell_line=FF:0000404
|fonse_cell_line_closure=FF:0000404
|fonse_cell_line_closure=FF:0000404
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|has_quality=
|has_quality=
|id=FF:12568-133H3
|id=FF:12568-133H3
|is_a=EFO:0002091;;FF:0000103;;FF:0000474
|is_a=EFO:0002091;;FF:0000474
|name=ST2 (Mesenchymal stem cells) cells, differentiation to osteocytes, 00hr30min, biol_rep3 (030mB3)
|is_obsolete=
|library_id=CNhs13309
|library_id_phase_based=2:CNhs13309
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12568
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12568
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520differentiation%2520to%2520osteocytes%252c%252000hr30min%252c%2520biol_rep3%2520%2528030mB3%2529.CNhs13309.12568-133H3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520differentiation%2520to%2520osteocytes%252c%252000hr30min%252c%2520biol_rep3%2520%2528030mB3%2529.CNhs13309.12568-133H3.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520differentiation%2520to%2520osteocytes%252c%252000hr30min%252c%2520biol_rep3%2520%2528030mB3%2529.CNhs13309.12568-133H3.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520differentiation%2520to%2520osteocytes%252c%252000hr30min%252c%2520biol_rep3%2520%2528030mB3%2529.CNhs13309.12568-133H3.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ST2%2520%2528Mesenchymal%2520stem%2520cells%2529%2520cells%252c%2520differentiation%2520to%2520osteocytes%252c%252000hr30min%252c%2520biol_rep3%2520%2528030mB3%2529.CNhs13309.12568-133H3.mm9.nobarcode.rdna.fa.gz
|name=ST2 (Mesenchymal stem cells) cells, differentiation to osteocytes
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs13309,LSID1021,release013,COMPLETED
|profile_hcage=CNhs13309,LSID1021,release013,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|rna_box=133
|rna_box=133
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|rna_sample_type=
|rna_sample_type=
|rna_tube_id=133H3
|rna_tube_id=133H3
|rna_weight_ug=5.50
|rna_weight_ug=5.5
|sample_age=
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=ST2
|sample_cell_line=ST2
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|sample_strain=
|sample_strain=
|sample_tissue=bone marrow
|sample_tissue=bone marrow
|time= 00hr30min
|timecourse=MSC_to_osteocyte_(mouse)
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12568-133H3;search_select_hide=table117:12568-133H3
}}
}}

Latest revision as of 18:40, 4 June 2020


Name:ST2 (Mesenchymal stem cells) cells, differentiation to osteocytes
Species:Mouse (Mus musculus)
Library ID:CNhs13309
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineST2
companyNA
collaborationYasushi Okazaki (Saitama medical college)
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  SAMD00021375
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13309 CAGE DRX023903 DRR026302
Accession ID Mm9

Library idBAMCTSS
CNhs13309 DRZ005554 DRZ006340
Accession ID Mm10

Library idBAMCTSS
CNhs13309 DRZ010169 DRZ010833
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
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>data

CNhs13309



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: CNhs13309This 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: CNhs13309This 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: CNhs13309


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)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000346 (30 minutes sample)
0000404 (mouse mesenchymal stem cell line: ST2 sample)
0000336 (osteogenic induction sample)
0000474 (mouse ST2 Mesenchymal stem cells, cells 30 minafter osteogenic induction 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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