Personal tools

FF:13303-142H9: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|accession_numbers=CAGE;DRX023771;DRR026170;DRZ005422;DRZ006208
|DRA_sample_Accession=CAGE@SAMD00021931
|accession_numbers=CAGE;DRX023771;DRR026170;DRZ005422;DRZ006208;DRZ010037;DRZ010701
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0000358,UBERON:0000307
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0002050,UBERON:0005423,UBERON:0001062,UBERON:0000358,UBERON:0000307
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000349,CL:0000255,CL:0000034,CL:0000351
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000349,CL:0000255,CL:0000034,CL:0000351
Line 11: Line 12:
|datafreeze_phase=2
|datafreeze_phase=2
|def=
|def=
|donor= biol_rep1
|fonse_cell_line=FF:0000626
|fonse_cell_line=FF:0000626
|fonse_cell_line_closure=FF:0000626
|fonse_cell_line_closure=FF:0000626
Line 43: Line 45:
|library_id=CNhs13530
|library_id=CNhs13530
|library_id_phase_based=2:CNhs13530
|library_id_phase_based=2:CNhs13530
|name=trophoblast stem cell line B1 differentiation, day06, biol_rep1
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13303
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13303
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day06%252c%2520biol_rep1.CNhs13530.13303-142H9.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day06%252c%2520biol_rep1.CNhs13530.13303-142H9.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day06%252c%2520biol_rep1.CNhs13530.13303-142H9.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day06%252c%2520biol_rep1.CNhs13530.13303-142H9.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/trophoblast%2520stem%2520cell%2520line%2520B1%2520differentiation%252c%2520day06%252c%2520biol_rep1.CNhs13530.13303-142H9.mm9.nobarcode.rdna.fa.gz
|name=trophoblast stem cell line B1 differentiation
|namespace=
|namespace=
|part_of=
|part_of=
Line 82: Line 93:
|sample_strain=
|sample_strain=
|sample_tissue=
|sample_tissue=
|timecourse=mouse_trophoblast_SCl_line
|time= day06
|timecourse=trophoblast_differentiation
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13303-142H9;search_select_hide=table117:13303-142H9
}}
}}

Latest revision as of 18:55, 4 June 2020


Name:trophoblast stem cell line B1 differentiation
Species:Mouse (Mus musculus)
Library ID:CNhs13530
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationHirohiko Kodeki(RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB1 +d6
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021931
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13530 CAGE DRX023771 DRR026170
Accession ID Mm9

Library idBAMCTSS
CNhs13530 DRZ005422 DRZ006208
Accession ID Mm10

Library idBAMCTSS
CNhs13530 DRZ010037 DRZ010701
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

CNhs13530



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: CNhs13530This 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: CNhs13530This 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: CNhs13530


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)
0002371 (somatic cell)
0000349 (extraembryonic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0000351 (trophoblast cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0001062 (anatomical entity)
0000358 (blastocyst)
0000307 (blastula)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000385 (6 days sample)
0000626 (trophoblast cell line sample)
0000641 (mouse trophoblast stem cell line B1 sample)
0000645 (tracheal ciliated cell differentiation sample)
0011213 (mouse trophoblast stem cell line B1 differentiation- day06 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:13303-142H9&oldid=4577727"