FF:12249-129H8

Name:	natural helper cells, IL2 treated, day15, biol_rep3
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	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 3 catalog number NA sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

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

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

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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: 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

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011524 mouse natural helper cells- IL2 treated, day15 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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000034 (stem cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0000255 (eukaryotic cell)
0000037 (hematopoietic stem cell)
0000566 (angioblastic mesenchymal cell)
0000837 (hematopoietic multipotent progenitor cell)
0002679 (natural helper lymphocyte)
0000051 (common lymphoid progenitor)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000160 (intestine)
0002384 (connective tissue)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0005291 (embryonic tissue)
0000925 (endoderm)
0006598 (presumptive structure)
0004185 (endodermal part of digestive tract)
0002532 (epiblast (generic))
0001555 (digestive tract)
0005409 (gastrointestinal system)
0007026 (primitive gut)
0006595 (presumptive endoderm)

FF: FANTOM5
NA

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
NA