FF:12250-129H9

Name:	unclassfied
Species:	Mouse (Mus musculus)
Library ID:	CNhs12510
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain NA tissue unclassifiable dev stage NA sex undefined_sex_type 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 4 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  SAMD00021243 Library accession numbers Library id Method Exp. accession id Run accession id CNhs12510 CAGE DRX023610 DRR026005 CAGE DRX023630 DRR026025 CAGE DRX024364 DRR026769 Accession ID Mm9 Library id BAM CTSS CNhs12510 DRZ005257 DRZ006047 DRZ005277 DRZ006067 DRZ006021 DRZ006801 Accession ID Mm10 Library id BAM CTSS CNhs12510

Download raw sequence, BAM & CTSS
Mm9 BAM CTSS [{{{mm9bam}}} download] [{{{mm9ctss}}} donwload] Mm10 BAM CTSS [{{{mm10bam}}} download] [{{{mm10ctss}}} 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

CNhs14386

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: CNhs14336This sample isn't target for the analysis
library id: CNhs14386This 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: CNhs14336This sample isn't target for the analysis
library id: CNhs14386This 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: CNhs14336
library id: CNhs14386

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)