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{{f5samples
{{f5samples
|id=FF:12249-129H8
|DRA_sample_Accession=CAGE@SAMD00021242
|name=natural helper cells, IL2 treated, day15, biol_rep3
|accession_numbers=CAGE;DRX023596;DRR025991;DRZ005243;DRZ006033;DRZ009984;DRZ010648!CAGE;DRX023609;DRR026004;DRZ005256;DRZ006046;DRZ009997;DRZ010661!CAGE;DRX023633;DRR026028;DRZ005280;DRZ006070;DRZ010021;DRZ010685
|sample_id=12249
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409
|rna_tube_id=129H8
|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=H8
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=3.00000
|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=2.21000
|rna_od260/280=1.92000
|sample_cell_type=natural helper cells
|sample_cell_line=
|sample_collaboration=Koyasu
|sample_experimental_condition=natural helper cells, stimulation with IL2 and IL35
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_weight_ug=2.96800
|rna_concentration=0.11872
|sample_note=Jan 20 librarian
|profile_hcage=CNhs12509,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:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026
|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:0000999,FF:0000292,FF:0000004,FF:0000350,FF:0000391,FF:0000636,FF:0000295,FF:0011524
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000134,CL:0000051,UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 39:
|fonse_treatment=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|fonse_treatment=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|fonse_treatment_closure=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|fonse_treatment_closure=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|has_quality=
|id=FF:12249-129H8
|is_a=EFO:0002091;;FF:0011524
|is_obsolete=
|library_id=CNhs12509!CNhs14335!CNhs14389
|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;12249
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12249
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL2%2520treated%252c%2520day15%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14389.12249-129H8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL2%2520treated%252c%2520day15%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14389.12249-129H8.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL2%2520treated%252c%2520day15%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14389.12249-129H8.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL2%2520treated%252c%2520day15%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14389.12249-129H8.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/natural%2520helper%2520cells%252c%2520IL2%2520treated%252c%2520day15%252c%2520biol_rep3%252c%2520tech_rep3.CNhs14389.12249-129H8.mm9.nobarcode.rdna.fa.gz
|name=natural helper cells, IL2 treated, day15, biol_rep3
|namespace=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12509&CNhs14335&CNhs14389,LSID918,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=129
|rna_catalog_number=
|rna_concentration=0.11872
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_lot_number=3
|rna_od260/230=2.21
|rna_od260/280=1.92
|rna_position=H8
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=129H8
|rna_weight_ug=2.968
|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=12249
|sample_note=Jan 20 librarian
|sample_sex=
|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=table111:12249-129H8;search_select_hide=table117:12249-129H8
}}
}}

Latest revision as of 18:37, 4 June 2020


Name:natural helper cells, IL2 treated, day15, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs12509,CNhs14335,CNhs14389
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 number3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021242
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12509 CAGE DRX023596 DRR025991
CNhs14335 CAGE DRX023609 DRR026004
CNhs14389 CAGE DRX023633 DRR026028
Accession ID Mm9

Library idBAMCTSS
CNhs12509 DRZ005243 DRZ006033
CNhs14335 DRZ005256 DRZ006046
CNhs14389 DRZ005280 DRZ006070
Accession ID Mm10

Library idBAMCTSS
CNhs12509 DRZ009984 DRZ010648
CNhs14335 DRZ009997 DRZ010661
CNhs14389 DRZ010021 DRZ010685
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

CNhs12509



CNhs14335



CNhs14389



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: CNhs12509This sample isn't target for the analysis
library id: CNhs14335This sample isn't target for the analysis
library id: CNhs14389This 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: CNhs12509This sample isn't target for the analysis
library id: CNhs14335This sample isn't target for the analysis
library id: CNhs14389This 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: CNhs12509
library id: CNhs14335
library id: CNhs14389


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)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000350 (experimentally modified sample)
0000391 (15 days sample)
0000636 (IL-2 treatment sample)
0000295 (mouse embryonic day 12 sample)
0011524 (mouse natural helper cells- IL2 treated, day15 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)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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