Personal tools

FF:11947-126B3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021213
|accession_numbers=CAGE;DRX024030;DRR026435;DRZ005687;DRZ006467;DRZ010302;DRZ010960
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000926,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0010316,UBERON:0005291
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000926,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0010316,UBERON:0005291
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 7: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316
Line 39: Line 43:
|is_a=FF:0200026
|is_a=FF:0200026
|is_obsolete=
|is_obsolete=
|library_id=CNhs14148
|library_id_phase_based=2:CNhs14148
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11947
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11947
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Mesoderm%252c%2520embryo%2520E8%252e5.CNhs14148.11947-126B3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Mesoderm%252c%2520embryo%2520E8%252e5.CNhs14148.11947-126B3.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Mesoderm%252c%2520embryo%2520E8%252e5.CNhs14148.11947-126B3.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Mesoderm%252c%2520embryo%2520E8%252e5.CNhs14148.11947-126B3.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Mesoderm%252c%2520embryo%2520E8%252e5.CNhs14148.11947-126B3.mm9.nobarcode.rdna.fa.gz
|name=Mesoderm, embryo E8.5
|name=Mesoderm, embryo E8.5
|namespace=
|namespace=
Line 78: Line 93:
|sample_strain=
|sample_strain=
|sample_tissue=ANATOMICAL SYSTEM
|sample_tissue=ANATOMICAL SYSTEM
|timecourse=HSC_development
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11947-126B3;search_select_hide=table117:11947-126B3
}}
}}

Latest revision as of 18:30, 4 June 2020


Name:Mesoderm, embryo E8.5
Species:Mouse (Mus musculus)
Library ID:CNhs14148
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationDaisuke Sugiyama
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  SAMD00021213
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14148 CAGE DRX024030 DRR026435
Accession ID Mm9

Library idBAMCTSS
CNhs14148 DRZ005687 DRZ006467
Accession ID Mm10

Library idBAMCTSS
CNhs14148 DRZ010302 DRZ010960
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

CNhs14148



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: CNhs14148This 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: CNhs14148This 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: CNhs14148


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000926 (mesoderm)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0001062 (anatomical entity)
0010316 (germ layer / neural crest)
0005291 (embryonic tissue)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0200024 (mouse embryonic day 8.5 sample)
0200026 (mouse mesoderm, embryonic day 8.5 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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11947-126B3&oldid=4576873"