FF:12252-129I2

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 strain NA tissue unclassifiable dev stage NA sex NA age NA cell type natural helper cells cell line NA company NA collaboration Koyasu External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number 6 catalog number NA sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method Sample accession id CAGE  SAMD00021245 Library accession numbers Library id Method Exp. accession id Run accession id CNhs12578 CAGE DRX023592 DRR025987 CNhs14331 CAGE DRX023605 DRR026000 CNhs14379 CAGE DRX023623 DRR026018 Accession ID Mm9 Library id BAM CTSS CNhs12578 DRZ005239 DRZ006029 CNhs14331 DRZ005252 DRZ006042 CNhs14379 DRZ005270 DRZ006060 Accession ID Mm10 Library id BAM CTSS CNhs12578 DRZ009980 DRZ010644 CNhs14331 DRZ009993 DRZ010657 CNhs14379 DRZ010011 DRZ010675

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download donwload

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

CNhs14379

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

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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: 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 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: 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 sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12578
library id: CNhs14331
library id: CNhs14379

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011139 mouse natural helper cells- IL33 treated- day02 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)
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)<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)