FF:14359-155I3: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
(17 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet= | |DRA_sample_Accession=CAGE@SAMD00021095 | ||
|ancestors_in_cell_lineage_facet= | |accession_numbers=CAGE;DRX022326;DRR024671;DRZ003493;DRZ003508;DRZ008239;DRZ008254 | ||
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0001062 | |||
|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:0200040,FF:0200035 | |||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
|creation_date= | |creation_date= | ||
|data_phase=2 | |||
|datafreeze_phase=2 | |||
|def= | |def= | ||
|donor= biol_rep1 | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
Line 36: | Line 42: | ||
|id=FF:14359-155I3 | |id=FF:14359-155I3 | ||
|is_a=EFO:0002091;;FF:0200035 | |is_a=EFO:0002091;;FF:0200035 | ||
|name=ES-46C embryonic stem cells, neuronal differentiation | |is_obsolete= | ||
|library_id=CNhs14106 | |||
|library_id_phase_based=2:CNhs14106 | |||
|microRNAs= | |||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;14359 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;14359 | |||
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ES-46C%2520embryonic%2520stem%2520cells%252c%2520neuronal%2520differentiation%252c%2520day02%252c%2520biol_rep1.CNhs14106.14359-155I3.mm10.nobarcode.bam | |||
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/ES-46C%2520embryonic%2520stem%2520cells%252c%2520neuronal%2520differentiation%252c%2520day02%252c%2520biol_rep1.CNhs14106.14359-155I3.mm10.nobarcode.ctss.bed.gz | |||
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ES-46C%2520embryonic%2520stem%2520cells%252c%2520neuronal%2520differentiation%252c%2520day02%252c%2520biol_rep1.CNhs14106.14359-155I3.mm9.nobarcode.bam | |||
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ES-46C%2520embryonic%2520stem%2520cells%252c%2520neuronal%2520differentiation%252c%2520day02%252c%2520biol_rep1.CNhs14106.14359-155I3.mm9.ctss.bed.gz | |||
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/ES-46C%2520embryonic%2520stem%2520cells%252c%2520neuronal%2520differentiation%252c%2520day02%252c%2520biol_rep1.CNhs14106.14359-155I3.mm9.nobarcode.rdna.fa.gz | |||
|name=ES-46C embryonic stem cells, neuronal differentiation | |||
|namespace= | |namespace= | ||
|part_of= | |part_of= | ||
Line 56: | Line 74: | ||
|rna_weight_ug=20 | |rna_weight_ug=20 | ||
|sample_age= | |sample_age= | ||
|sample_category=time courses | |||
|sample_cell_catalog= | |sample_cell_catalog= | ||
|sample_cell_line=46C | |sample_cell_line=46C | ||
Line 71: | Line 90: | ||
|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= | ||
|time= day02 | |||
|timecourse=ES_to_neuron | |||
|top_motifs= | |top_motifs= | ||
|xref= | |||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:14359-155I3;search_select_hide=table117:14359-155I3 | |||
}} | }} |
Latest revision as of 19:07, 4 June 2020
Name: | ES-46C embryonic stem cells, neuronal differentiation |
---|---|
Species: | Mouse (Mus musculus) |
Library ID: | CNhs14106 |
Sample type: | time courses |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
ZENBU report : | link |
Additional information | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
CAGE Accession numbers | ||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Download raw sequence, BAM & CTSS | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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
CNhs14106
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: CNhs14106This 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: CNhs14106This 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: CNhs14106
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0200035 ES-46C embryonic stem cells, neuronal differentiation sample
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)
0200040 (ES-46C derived epistem cells sample)
0200035 (ES-46C embryonic stem cells, neuronal differentiation 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