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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00022228
|accession_numbers=CAGE;DRX024294;DRR026699;DRZ005951;DRZ006731;DRZ010566;DRZ011224
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0002384,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0002384,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0002371,CL:0000499,CL:0000327,CL:0000255,CL:0000057,CL:0000632
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0002371,CL:0000499,CL:0000327,CL:0000255,CL:0000057,CL:0000632
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000101,FF:0000103,FF:0000001,FF:0200014
|ancestors_in_ff_facet=FF:0000101,FF:0000103,FF:0000001,FF:0200014
|data_phase=2
|datafreeze_phase=2
|ffid_belonging_in_development=CL:0000134
|ffid_belonging_in_development=CL:0000134
|has_quality=
|has_quality=
|id=FF:13612-146G3
|id=FF:13612-146G3
|is_a=CL:0000632;;FF:0000103;;FF:0200014
|is_a=CL:0000632;;FF:0000103;;FF:0200014
|library_id=CNhs14392
|library_id_phase_based=2:CNhs14392
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13612
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13612
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.LQhCAGE/hepatic%2520stellate%2520cells%252c%2520sham%2520operation%252c%2520biol_rep3.CNhs14392.13612-146G3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.LQhCAGE/hepatic%2520stellate%2520cells%252c%2520sham%2520operation%252c%2520biol_rep3.CNhs14392.13612-146G3.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.LQhCAGE/hepatic%2520stellate%2520cells%252c%2520sham%2520operation%252c%2520biol_rep3.CNhs14392.13612-146G3.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.LQhCAGE/hepatic%2520stellate%2520cells%252c%2520sham%2520operation%252c%2520biol_rep3.CNhs14392.13612-146G3.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.LQhCAGE/hepatic%2520stellate%2520cells%252c%2520sham%2520operation%252c%2520biol_rep3.CNhs14392.13612-146G3.mm9.nobarcode.rdna.fa.gz
|name=hepatic stellate cells, sham operation, biol_rep3
|name=hepatic stellate cells, sham operation, biol_rep3
|part_of=
|part_of=
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|rna_weight_ug=0.55
|rna_weight_ug=0.55
|sample_age=
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=UNDEFINED_CELL_LINE
|sample_cell_line=UNDEFINED_CELL_LINE
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|sample_strain=UNDEFINED_STRAIN
|sample_strain=UNDEFINED_STRAIN
|sample_tissue=UNDEFINED_TISSUE_TYPE
|sample_tissue=UNDEFINED_TISSUE_TYPE
|timecourse=Liver_regeneration
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13612-146G3;search_select_hide=table117:13612-146G3
}}
}}

Latest revision as of 19:03, 4 June 2020


Name:hepatic stellate cells, sham operation, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs14392
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainUNDEFINED_STRAIN
tissueUNDEFINED_TISSUE_TYPE
dev stageUNDEFINED_DEV_STAGE
sexUNDEFINED_SEX_TYPE
ageNA
cell typehepatic stellate cell
cell lineUNDEFINED_CELL_LINE
companyNA
collaborationUNDEFINED_COLLABORATION
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022228
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14392 CAGE DRX024294 DRR026699
Accession ID Mm9

Library idBAMCTSS
CNhs14392 DRZ005951 DRZ006731
Accession ID Mm10

Library idBAMCTSS
CNhs14392 DRZ010566 DRZ011224
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

CNhs14392



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: CNhs14392This 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: CNhs14392This 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: CNhs14392


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)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0000632 (hepatic stellate cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0002384 (connective tissue)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0200014 (sham operation 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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