Personal tools

Difference between revisions of "FF:12252-129I2"

From FANTOM5_SSTAR

Jump to: navigation, search
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
{{f5samples
 
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
+
|DRA_sample_Accession=CAGE@SAMD00021245
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000548,CL:0000034,CL:0002032,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000542,CL:0000219,CL:0000004,CL:0000134,CL:0000738,CL:0002087,CL:0000255,CL:0000037,CL:0000566,CL:0000837,CL:0002679,CL:0000051
+
|accession_numbers=CAGE;DRX023592;DRR025987;DRZ005239;DRZ006029;DRZ009980;DRZ010644!CAGE;DRX023605;DRR026000;DRZ005252;DRZ006042;DRZ009993;DRZ010657!CAGE;DRX023623;DRR026018;DRZ005270;DRZ006060;DRZ010011;DRZ010675
 +
|ancestors_in_anatomy_facet=
 +
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000738,CL:0002087,CL:0002242,CL:0000255,CL:0002679
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
 +
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000382,FF:0000637,FF:0011139
 
|comment=
 
|comment=
 
|created_by=
 
|created_by=
 
|creation_date=
 
|creation_date=
 +
|data_phase=2
 +
|datafreeze_phase=2
 
|def=
 
|def=
 +
|ffid_belonging_in_development=CL:0000134,CL:0000051
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=
Line 37: Line 43:
 
|is_a=EFO:0002091;;FF:0011139
 
|is_a=EFO:0002091;;FF:0011139
 
|is_obsolete=
 
|is_obsolete=
 +
|library_id=CNhs12578!CNhs14331!CNhs14379
 +
|library_id_phase_based=2:
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12252
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12252
 +
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL33%2520treated%252c%2520day02%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14379.12252-129I2.mm10.nobarcode.bam
 +
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL33%2520treated%252c%2520day02%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14379.12252-129I2.mm10.nobarcode.ctss.bed.gz
 +
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL33%2520treated%252c%2520day02%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14379.12252-129I2.mm9.nobarcode.bam
 +
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL33%2520treated%252c%2520day02%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14379.12252-129I2.mm9.ctss.bed.gz
 +
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL33%2520treated%252c%2520day02%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14379.12252-129I2.mm9.nobarcode.rdna.fa.gz
 
|name=natural helper cells, IL33 treated, day02, biol_rep3
 
|name=natural helper cells, IL33 treated, day02, biol_rep3
 
|namespace=
 
|namespace=
Line 42: Line 59:
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
 
|profile_hcage=CNhs12578&CNhs14331&CNhs14379,LSID917,release012,COMPLETED
 
|profile_hcage=CNhs12578&CNhs14331&CNhs14379,LSID917,release012,COMPLETED
|profile_rnaseq=,,,
+
|profile_rnaseq=
 
|profile_srnaseq=,,,
 
|profile_srnaseq=,,,
 
|rna_box=129
 
|rna_box=129
Line 57: Line 74:
 
|rna_weight_ug=7.11125
 
|rna_weight_ug=7.11125
 
|sample_age=
 
|sample_age=
 +
|sample_category=primary cells
 
|sample_cell_catalog=
 
|sample_cell_catalog=
 
|sample_cell_line=
 
|sample_cell_line=
Line 77: Line 95:
 
|top_motifs=
 
|top_motifs=
 
|xref=
 
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12252-129I2;search_select_hide=table117:12252-129I2
 
}}
 
}}

Latest revision as of 09:37, 4 June 2020


Name:natural helper cells, IL33 treated, day02, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs12578,CNhs14331,CNhs14379
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexNA
ageNA
cell typenatural helper cells
cell lineNA
companyNA
collaborationKoyasu
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number6
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021245
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12578 CAGE DRX023592 DRR025987
CNhs14331 CAGE DRX023605 DRR026000
CNhs14379 CAGE DRX023623 DRR026018
Accession ID Mm9

Library idBAMCTSS
CNhs12578 DRZ005239 DRZ006029
CNhs14331 DRZ005252 DRZ006042
CNhs14379 DRZ005270 DRZ006060
Accession ID Mm10

Library idBAMCTSS
CNhs12578 DRZ009980 DRZ010644
CNhs14331 DRZ009993 DRZ010657
CNhs14379 DRZ010011 DRZ010675
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.
Analyst:NA

link to dataset.
data

CNhs12578



CNhs14331



CNhs14379



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12578This sample isn't target for the analysis
library id: CNhs14331This sample isn't target for the analysis
library id: CNhs14379This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12578This sample isn't target for the analysis
library id: CNhs14331This sample isn't target for the analysis
library id: CNhs14379This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs12578
library id: CNhs14331
library id: CNhs14379


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0002679 (natural helper lymphocyte)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000382 (2 days sample)
0000637 (IL-33 treatment sample)
0011139 (mouse natural helper cells- IL33 treated- day02 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)