FF:12215-129E1

Name:	Inner ear stem cells, 1st generation stem cells, 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 organ of corti dev stage NA sex NA age NA cell type hair cell, organ of corti, inner 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 NA 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

CNhs11929

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: CNhs11929This 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: CNhs11929This 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: CNhs11929

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000256 Inner ear stem cell (1st generation stem cell) 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)
0000197 (receptor 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)
0000066 (epithelial cell)
0002371 (somatic cell)
0002319 (neural cell)
0000221 (ectodermal cell)
0000393 (electrically responsive cell)
0000006 (neuronal receptor cell)
0002374 (ear hair cell)
0002491 (auditory epithelial cell)
0000031 (neuroblast)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000202 (auditory hair cell)
0000199 (mechanoreceptor cell)
0000098 (sensory epithelial cell)
0000855 (sensory hair cell)
0000589 (cochlear inner hair cell)
0000133 (neurectodermal cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002100 (trunk)
0000483 (epithelium)
0001474 (bone element)
0000033 (head)
0000926 (mesoderm)
0000479 (tissue)
0000058 (duct)
0000064 (organ part)
0000073 (regional part of nervous system)
0004121 (ectoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
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)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0005291 (embryonic tissue)
0000020 (sense organ)
0000075 (subdivision of skeletal system)
0000485 (simple columnar epithelium)
0008193 (pneumatized bone)
0005744 (cranial conduit)
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)
0005253 (head mesenchyme)
0002532 (epiblast (generic))
0001017 (central nervous system)
0002227 (spiral organ of cochlea)
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)
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)
0001849 (membranous labyrinth)
0002499 (cochlear labyrinth)
0001855 (cochlear duct of membranous labyrinth)
0001703 (neurocranium)
0003077 (paraxial mesoderm)
0009142 (entire embryonic mesenchyme)
0003069 (otic placode)
0003051 (ear vesicle)
0004288 (skeleton)
0004637 (otic capsule)
0006601 (presumptive ectoderm)
0006603 (presumptive mesoderm)
0004761 (cartilaginous neurocranium)
0010113 (future membranous labyrinth)
0003089 (sclerotome)
0003059 (presomitic mesoderm)
0009123 (otic cup)
0007282 (presumptive segmental plate)
0009618 (trunk paraxial mesoderm)
0007285 (presumptive paraxial mesoderm)
0009617 (head paraxial mesoderm)
0005641 (otocyst epithelium)

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