Personal tools

FF:12254-129I4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:12254-129I4 |name=natural helper cells, IL33 treated, 01hr, biol_rep2 |sample_id=12254 |rna_tube_id=129I4 |rna_box=129 |rna_position=I4 |sample_cell_...")
 
No edit summary
 
(21 intermediate revisions by 2 users not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:12254-129I4
|DRA_sample_Accession=CAGE@SAMD00021247
|name=natural helper cells, IL33 treated, 01hr, biol_rep2
|accession_numbers=CAGE;DRX023612;DRR026007;DRZ005259;DRZ006049;DRZ010000;DRZ010664!CAGE;DRX023628;DRR026023;DRZ005275;DRZ006065;DRZ010016;DRZ010680!CAGE;DRX024366;DRR026771;DRZ006023;DRZ006803;DRZ010638;DRZ011296
|sample_id=12254
|ancestors_in_anatomy_facet=
|rna_tube_id=129I4
|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
|rna_box=129
|rna_position=I4
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=8.00000
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_dev_stage=
|sample_tissue=unclassifiable
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=1.98000
|rna_od260/280=1.84000
|sample_cell_type=natural helper cells
|sample_cell_line=
|sample_collaboration=Koyasu
|sample_experimental_condition=natural helper cells, stimulation with IL2 and IL40
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_weight_ug=2.22650
|rna_concentration=0.08906
|sample_note=Jan 20 librarian
|profile_hcage=CNhs12512,LSID918,release012,MAPPING
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000837,CL:0000988,CL:0002032,CL:0002087,CL:0002320,CL:0002371,CL:0002679
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000358,FF:0000637,FF:0011138
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000134,CL:0000051
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 39:
|fonse_treatment=EFO:0000369,FF:0000637,FF:0011138,FF:12254-129I4
|fonse_treatment=EFO:0000369,FF:0000637,FF:0011138,FF:12254-129I4
|fonse_treatment_closure=EFO:0000369,FF:0000637,FF:0011138,FF:12254-129I4
|fonse_treatment_closure=EFO:0000369,FF:0000637,FF:0011138,FF:12254-129I4
|has_quality=
|id=FF:12254-129I4
|is_a=EFO:0002091;;FF:0011138
|is_obsolete=
|library_id=CNhs14338!CNhs14384!CNhs12512
|library_id_phase_based=2:CNhs12512
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12254
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12254
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL33%2520treated%252c%252001hr%252c%2520biol_rep2%252c%2520tech_rep3.CNhs14384.12254-129I4.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%252001hr%252c%2520biol_rep2%252c%2520tech_rep3.CNhs14384.12254-129I4.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%252001hr%252c%2520biol_rep2%252c%2520tech_rep3.CNhs14384.12254-129I4.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL33%2520treated%252c%252001hr%252c%2520biol_rep2%252c%2520tech_rep3.CNhs14384.12254-129I4.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%252001hr%252c%2520biol_rep2%252c%2520tech_rep3.CNhs14384.12254-129I4.mm9.nobarcode.rdna.fa.gz
|name=unclassfied
|namespace=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs14338&CNhs14384,LSID918,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=129
|rna_catalog_number=
|rna_concentration=0.08906
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_lot_number=8
|rna_od260/230=1.98
|rna_od260/280=1.84
|rna_position=I4
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=129I4
|rna_weight_ug=2.2265
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=natural helper cells
|sample_collaboration=Koyasu
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=natural helper cells, stimulation with IL2 and IL33
|sample_id=12254
|sample_note=
|sample_sex=undefined_sex_type
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=unclassifiable
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12254-129I4;search_select_hide=table117:12254-129I4
}}
}}

Latest revision as of 18:37, 4 June 2020


Name:unclassfied
Species:Mouse (Mus musculus)
Library ID:CNhs14338,CNhs14384,CNhs12512
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexundefined_sex_type
ageNA
cell typenatural helper cells
cell lineNA
companyNA
collaborationKoyasu
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021247
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14338 CAGE DRX023612 DRR026007
CNhs14384 CAGE DRX023628 DRR026023
CNhs12512 CAGE DRX024366 DRR026771
Accession ID Mm9

Library idBAMCTSS
CNhs14338 DRZ005259 DRZ006049
CNhs14384 DRZ005275 DRZ006065
CNhs12512 DRZ006023 DRZ006803
Accession ID Mm10

Library idBAMCTSS
CNhs14338 DRZ010000 DRZ010664
CNhs14384 DRZ010016 DRZ010680
CNhs12512 DRZ010638 DRZ011296
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

CNhs14338



CNhs14384



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: CNhs14338This sample isn't target for the analysis
library id: CNhs14384This 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: CNhs14338This sample isn't target for the analysis
library id: CNhs14384This 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: CNhs14338
library id: CNhs14384


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)
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)
0000358 (1 hr sample)
0000637 (IL-33 treatment sample)
0011138 (mouse natural helper cells- IL33 treated- 01hr 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
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:12254-129I4&oldid=4576986"