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{{f5samples
{{f5samples
|id=FF:12248-129H7
|DRA_sample_Accession=CAGE@SAMD00021241
|name=natural helper cells, IL2 treated, day15, biol_rep2
|accession_numbers=CAGE;DRX023595;DRR025990;DRZ005242;DRZ006032;DRZ009983;DRZ010647!CAGE;DRX023608;DRR026003;DRZ005255;DRZ006045;DRZ009996;DRZ010660!CAGE;DRX023632;DRR026027;DRZ005279;DRZ006069;DRZ010020;DRZ010684
|sample_id=12248
|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=129H7
|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=H7
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=2
|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=2.2
|rna_od260/280=1.92
|sample_cell_type=natural helper cells
|sample_cell_line=
|sample_collaboration=Koyasu
|sample_experimental_condition=natural helper cells, stimulation with IL2 and IL34
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_weight_ug=5.08075
|rna_concentration=0.20323
|sample_note=Jan 20 librarian
|profile_hcage=CNhs12508,LSID918,release012,COMPLETED
|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 66: Line 39:
|fonse_treatment=EFO:0000369,FF:0000636,FF:0011524,FF:12248-129H7
|fonse_treatment=EFO:0000369,FF:0000636,FF:0011524,FF:12248-129H7
|fonse_treatment_closure=EFO:0000369,FF:0000636,FF:0011524,FF:12248-129H7
|fonse_treatment_closure=EFO:0000369,FF:0000636,FF:0011524,FF:12248-129H7
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011524
|id=FF:12248-129H7
|is_a=EFO:0002091;;FF:0011524
|is_obsolete=
|library_id=CNhs12508!CNhs14334!CNhs14388
|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;12248
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12248
|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_rep2%252c%2520tech_rep3.CNhs14388.12248-129H7.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_rep2%252c%2520tech_rep3.CNhs14388.12248-129H7.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_rep2%252c%2520tech_rep3.CNhs14388.12248-129H7.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_rep2%252c%2520tech_rep3.CNhs14388.12248-129H7.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_rep2%252c%2520tech_rep3.CNhs14388.12248-129H7.mm9.nobarcode.rdna.fa.gz
|name=natural helper cells, IL2 treated, day15, biol_rep2
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12508&CNhs14334&CNhs14388,LSID918,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=129
|rna_catalog_number=
|rna_concentration=0.20323
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_lot_number=2
|rna_od260/230=2.2
|rna_od260/280=1.92
|rna_position=H7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=129H7
|rna_weight_ug=5.08075
|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=12248
|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=table111:12248-129H7;search_select_hide=table117:12248-129H7
}}
}}

Latest revision as of 18:37, 4 June 2020


Name:natural helper cells, IL2 treated, day15, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs12508,CNhs14334,CNhs14388
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 number2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021241
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12508 CAGE DRX023595 DRR025990
CNhs14334 CAGE DRX023608 DRR026003
CNhs14388 CAGE DRX023632 DRR026027
Accession ID Mm9

Library idBAMCTSS
CNhs12508 DRZ005242 DRZ006032
CNhs14334 DRZ005255 DRZ006045
CNhs14388 DRZ005279 DRZ006069
Accession ID Mm10

Library idBAMCTSS
CNhs12508 DRZ009983 DRZ010647
CNhs14334 DRZ009996 DRZ010660
CNhs14388 DRZ010020 DRZ010684
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

CNhs12508



CNhs14334



CNhs14388



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: CNhs12508This sample isn't target for the analysis
library id: CNhs14334This sample isn't target for the analysis
library id: CNhs14388This 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: CNhs12508This sample isn't target for the analysis
library id: CNhs14334This sample isn't target for the analysis
library id: CNhs14388This 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: CNhs12508
library id: CNhs14334
library id: CNhs14388


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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