Personal tools

FF:13271-142E4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(21 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001013,UBERON:0001062,UBERON:0002384
|DRA_sample_Accession=CAGE@SAMD00021902
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371,CL:0002570
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00021902
|accession_numbers=CAGE;DRX023210;DRR025549;DRZ003974;DRZ004857;DRZ008715;DRZ009598
|accession_numbers_RNASeq=sRNA-Seq;DRX036558;DRR040612;DRZ006977
|ancestors_in_anatomy_facet=UBERON:0001013,UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|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:0002570
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000350,FF:0000329,FF:0000096,FF:0000387,FF:0000704
|comment=
|comment=
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|donor= biol_rep1
|ffid_belonging_in_development=CL:0000134
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 34: Line 43:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/mesenchymal%2520stem%2520cells%2520%2528adipose%2520derived%2529%252c%2520adipogenic%2520induction%252c%2520day08%252c%2520biol_rep1.CNhs13625.13271-142E4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/mesenchymal%2520stem%2520cells%2520%2528adipose%2520derived%2529%252c%2520adipogenic%2520induction%252c%2520day08%252c%2520biol_rep1.CNhs13625.13271-142E4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/mesenchymal%2520stem%2520cells%2520%2528adipose%2520derived%2529%252c%2520adipogenic%2520induction%252c%2520day08%252c%2520biol_rep1.CNhs13625.13271-142E4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/mesenchymal%2520stem%2520cells%2520%2528adipose%2520derived%2529%252c%2520adipogenic%2520induction%252c%2520day08%252c%2520biol_rep1.CNhs13625.13271-142E4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/mesenchymal%2520stem%2520cells%2520%2528adipose%2520derived%2529%252c%2520adipogenic%2520induction%252c%2520day08%252c%2520biol_rep1.CNhs13625.13271-142E4.hg38.nobarcode.ctss.bed.gz
|id=FF:13271-142E4
|id=FF:13271-142E4
|is_a=EFO:0002091;;FF:0000210;;FF:0000704
|is_a=EFO:0002091;;FF:0000704
|name=mesenchymal stem cells (adipose derived), adipogenic induction, day08, biol_rep1
|is_obsolete=
|library_id=CNhs13625
|library_id_phase_based=2:CNhs13625
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13271
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10065.CCGTCC.13271
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13271
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10065.CCGTCC.13271
|name=mesenchymal stem cells (adipose derived), adipogenic induction
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
Line 45: Line 68:
|rna_box=142
|rna_box=142
|rna_catalog_number=
|rna_catalog_number=
|rna_concentration=0.40
|rna_concentration=0.4
|rna_extraction_protocol=
|rna_extraction_protocol=
|rna_lot_number=F205
|rna_lot_number=F205
Line 53: Line 76:
|rna_rin=
|rna_rin=
|rna_sample_type=
|rna_sample_type=
|rna_tube_id=142E4
|rna_tube_id=1.42E+06
|rna_weight_ug=5.00
|rna_weight_ug=5
|rnaseq_library_id=SRhi10065.CCGTCC
|sample_age=16
|sample_age=16
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_line=
Line 74: Line 99:
|sample_strain=
|sample_strain=
|sample_tissue=
|sample_tissue=
|time= day08
|timecourse=MSC_to_adipocyte_(human)
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13271-142E4;search_select_hide=table117:FF:13271-142E4
}}
}}

Latest revision as of 18:55, 4 June 2020


Name:mesenchymal stem cells (adipose derived), adipogenic induction
Species:Human (Homo sapiens)
Library ID:CNhs13625
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age16
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationPeter Arner(Karolinska)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberF205
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021902
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13625 CAGE DRX023210 DRR025549
Accession ID Hg19

Library idBAMCTSS
CNhs13625 DRZ003974 DRZ004857
Accession ID Hg38

Library idBAMCTSS
CNhs13625 DRZ008715 DRZ009598
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00021902
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10065.CCGTCC sRNA-Seq DRX036558 DRR040612
Accession ID Hg19

Library idBAMCTSS
SRhi10065.CCGTCC DRZ006977





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: CNhs13625This 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: CNhs13625This 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: CNhs13625


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)
0002570 (mesenchymal stem cell of adipose)

UBERON: Anatomy
0001013 (adipose tissue)
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000350 (experimentally modified sample)
0000329 (adipogenic induction sample)
0000096 (human mesenchymal stem cell of adipose sample)
0000387 (8 days sample)
0000704 (human mesenchymal stem cells adipose derived, 8 days after adipogenic 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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:13271-142E4&oldid=4577695"