FF:11959-126C6

Name:	Neurons - spiral ganglion, pool1
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 ANATOMICAL SYSTEM dev stage NA sex NA age NA cell type NA cell line NA company NA collaboration Albert Edge (Department of Otolaryngology, Harvard Medical School) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type total RNA extraction protocol (Details) NA

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

CNhs14147

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: CNhs14147This 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: CNhs14147This 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: CNhs14147

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
FF:0200030 neurons - spiral ganglion 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)
0000540 (neuron)
0000055 (non-terminally differentiated cell)
0000047 (neuronal stem cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000034 (stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002319 (neural cell)
0000221 (ectodermal cell)
0000393 (electrically responsive cell)
0000031 (neuroblast)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000133 (neurectodermal cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002100 (trunk)
0000483 (epithelium)
0001474 (bone element)
0000033 (head)
0003714 (neural tissue)
0000926 (mesoderm)
0000395 (cochlear ganglion)
0000479 (tissue)
0002346 (neurectoderm)
0000064 (organ part)
0000073 (regional part of nervous system)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004765 (skeletal element)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005162 (multi cell component structure)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001714 (cranial ganglion)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0005291 (embryonic tissue)
0000020 (sense organ)
0000122 (neuron projection bundle)
0000075 (subdivision of skeletal system)
0000485 (simple columnar epithelium)
0008193 (pneumatized bone)
0000045 (ganglion)
0003338 (ganglion of peripheral nervous system)
0001021 (nerve)
0003104 (mesenchyme)
0001032 (sensory system)
0008001 (irregular bone)
0005085 (ectodermal placode)
0007497 (developing epithelial placode)
0009955 (neurogenic placode)
0003067 (dorsolateral placode)
0002546 (cranial placode)
0005256 (trunk mesenchyme)
0001048 (primordium)
0007914 (head or neck bone)
0003457 (head bone)
0004766 (cranial bone)
0006598 (presumptive structure)
0001785 (cranial nerve)
0005157 (epithelial fold)
0003099 (cranial neural crest)
0005913 (zone of bone organ)
0005253 (head mesenchyme)
0002532 (epiblast (generic))
0001017 (central nervous system)
0000010 (peripheral nervous system)
0002329 (somite)
0001846 (internal ear)
0001016 (nervous system)
0003128 (cranium)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0000924 (ectoderm)
0002827 (vestibulocochlear ganglion)
0004456 (entire sense organ system)
0002241 (chondrocranium)
0002105 (vestibulo-auditory system)
0001678 (temporal bone)
0003129 (skull)
0001694 (petrous part of temporal bone)
0004681 (vestibular system)
0001839 (bony labyrinth)
0001690 (ear)
0001844 (cochlea)
0001703 (neurocranium)
0003075 (neural plate)
0003077 (paraxial mesoderm)
0002342 (neural crest)
0009142 (entire embryonic mesenchyme)
0003069 (otic placode)
0003051 (ear vesicle)
0004288 (skeleton)
0003869 (presumptive ganglion)
0006601 (presumptive ectoderm)
0006603 (presumptive mesoderm)
0004761 (cartilaginous neurocranium)
0003089 (sclerotome)
0003059 (presomitic mesoderm)
0005062 (neural fold)
0003249 (epithelium of otic placode)
0005565 (facio-acoustic neural crest)
0009123 (otic cup)
0007282 (presumptive segmental plate)
0009618 (trunk paraxial mesoderm)
0007284 (presumptive neural plate)
0007285 (presumptive paraxial mesoderm)
0009617 (head paraxial mesoderm)

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