Personal tools

FF:14353-155H6: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00022322
|accession_numbers=CAGE;DRX023999;DRR026404;DRZ005656;DRZ006436;DRZ010271;DRZ010929
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0000004,CL:0000255,CL:0002322
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002321,CL:0000255,CL:0000034,CL:0002322
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000001,FF:0101581,FF:0100669,FF:0200031,FF:0200033
|comment=
|comment=
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|fonse_cell_line=
|fonse_cell_line=
Line 37: Line 42:
|is_a=EFO:0002091;;FF:0200033
|is_a=EFO:0002091;;FF:0200033
|is_obsolete=
|is_obsolete=
|library_id=CNhs14100
|library_id_phase_based=2:CNhs14100
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;14353
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;14353
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ES-Ert2%2520embryonic%2520stem%2520cells%252c%2520untreated%2520control%252c%252048hr%252c%2520biol_rep3.CNhs14100.14353-155H6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ES-Ert2%2520embryonic%2520stem%2520cells%252c%2520untreated%2520control%252c%252048hr%252c%2520biol_rep3.CNhs14100.14353-155H6.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ES-Ert2%2520embryonic%2520stem%2520cells%252c%2520untreated%2520control%252c%252048hr%252c%2520biol_rep3.CNhs14100.14353-155H6.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ES-Ert2%2520embryonic%2520stem%2520cells%252c%2520untreated%2520control%252c%252048hr%252c%2520biol_rep3.CNhs14100.14353-155H6.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ES-Ert2%2520embryonic%2520stem%2520cells%252c%2520untreated%2520control%252c%252048hr%252c%2520biol_rep3.CNhs14100.14353-155H6.mm9.nobarcode.rdna.fa.gz
|name=ES-Ert2 embryonic stem cells, untreated control, 48hr, biol_rep3
|name=ES-Ert2 embryonic stem cells, untreated control, 48hr, biol_rep3
|namespace=
|namespace=
Line 57: Line 73:
|rna_weight_ug=15
|rna_weight_ug=15
|sample_age=
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=Ert2 ES
|sample_cell_line=Ert2 ES
Line 72: Line 89:
|sample_note=Change category into timecourse
|sample_note=Change category into timecourse
|sample_sex=
|sample_sex=
|sample_species=Mus musculus
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_strain=
|sample_tissue=
|sample_tissue=
|timecourse=ES_series
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:14353-155H6;search_select_hide=table117:14353-155H6
}}
}}

Latest revision as of 19:07, 4 June 2020


Name:ES-Ert2 embryonic stem cells, untreated control, 48hr, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs14100
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageES
sexNA
ageNA
cell typeembryonic stem cell
cell lineErt2 ES
companyNA
collaborationAna Pombo and Kelly Morris (MRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022322
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14100 CAGE DRX023999 DRR026404
Accession ID Mm9

Library idBAMCTSS
CNhs14100 DRZ005656 DRZ006436
Accession ID Mm10

Library idBAMCTSS
CNhs14100 DRZ010271 DRZ010929
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

CNhs14100



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: CNhs14100This 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: CNhs14100This 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: CNhs14100


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)
0002321 (embryonic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002322 (embryonic stem cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000001 (sample)
0101581 (embryonic stem cell line sample)
0100669 (embryonic cell line sample)
0200031 (ES-OS25 embryonic stem cells sample)
0200033 (ES-OS25 embryonic stem cells, untreated 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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:14353-155H6&oldid=4578168"