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Mouse utricle hair bundles and whole utricles—Velos

ABSTRACT: Purified utricle hair bundles and utricular epithelium from P21-P25 mouse inner ears were analyzed by LC-MS/MS to determine the abundant and enriched proteins of the hair bundle. This dataset used a Thermo LTQ Velos mass spectrometer for protein detection.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Macular Hair Cell, Utricle, Inner Ear

SUBMITTER: Peter Barr-Gillespie

LAB HEAD: Peter Barr-Gillespie

PROVIDER: PXD002415 | Pride | 2015-11-17

REPOSITORIES: Pride

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			Action	DRS
	GIL1591_P21_CD1_Bun1-1_10-15ng_75um_140_20141004_VE2.raw	Raw
	GIL1591_P21_CD1_Bun1-2_10-15ng_75um_140_20141004_VE2.raw	Raw
	GIL1591_P21_CD1_Bun1-3_10-15ng_75um_140_20141004_VE2.raw	Raw
	GIL1591_P21_CD1_Bun1-4_10-15ng_75um_140_20141004_VE2.raw	Raw
	GIL1591_P21_CD1_Bun1-5_10-15ng_75um_140_20141004_VE2.raw	Raw

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Publications

Hair-bundle proteomes of avian and mammalian inner-ear utricles.

Wilmarth Phillip A PA Krey Jocelyn F JF Shin Jung-Bum JB Choi Dongseok D David Larry L LL Barr-Gillespie Peter G PG

Scientific data 20151208

Examination of multiple proteomics datasets within or between species increases the reliability of protein identification. We report here proteomes of inner-ear hair bundles from three species (chick, mouse, and rat), which were collected on LTQ or LTQ Velos ion-trap mass spectrometers; the constituent proteins were quantified using MS2 intensities, which are the summed intensities of all peptide fragmentation spectra matched to a protein. The data are available via ProteomeXchange with identifi ...[more]

PMID: 26645194

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Rat utricle hair bundles and whole utricles—LTQ

Project description:Purified utricle hair bundles and utricular epithelium from P3-P7 rat inner ears were analyzed by LC-MS/MS to determine the abundant and enriched proteins of the hair bundle. This dataset used a Thermo LTQ mass spectrometer for protein detection.

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Chick utricle hair bundles and utricular epithelium—Velos

Project description:Purified hair bundles and utricular epithelium from E19-E20 chick inner ears were analyzed by LC-MS/MS to determine the abundant and enriched proteins of the hair bundle. This dataset used a Thermo LTQ Velos mass spectrometer for protein detection.

2015-11-17 | PXD002414 | Pride

Chick utricle hair bundles and utricular epithelium—LTQ

2015-11-17 | PXD002410 | Pride

Reprocessed: Chick utricle hair bundles and utricular epithelium—Orbitrap

Project description:This is a reanalysis of PXD000104. Purified hair bundles and utricular epithelium from E19-E20 chick inner ears were analyzed by LC-MS/MS to determine the abundant and enriched proteins of the hair bundle. This dataset used a Thermo Orbitrap Elite mass spectrometer for protein detection.

2015-11-17 | PXD002445 | Pride

Cell-type identity of the avian utricle

Project description:The avian utricle, a vestibular organ of the inner ear, displays turnover of sensory hair cells throughout life. This is in sharp contrast to the mammalian utricle, which shows limited regenerative capacity. Here, we use single-cell RNA-sequencing to identify distinct marker genes for the different sensory hair cell subtypes of the chicken utricle, which we validated in situ . We provide markers for spatially distinct supporting cell populations, and identified two transitional cell populations of dedifferentiating supporting cells and developing hair cells. Trajectory reconstruction resulted in an inventory of gene expression dynamics of natural hair cell generation in the avian utricle.

2022-09-07 | GSE212831 | GEO

Gene Expression from hair cells and supporting cells in chick utricle

Project description:In adult mammals, hair cell loss is irreversible and may result in hearing and balance deficits. In contrast, birds can regenerate hair cells through differentiation of supporting cells and restore inner ear function, suggesting that hair cell progenitors are present in the population of supporting cells. We used microarrays to identify novel genes related to the regeneration in the chicken utricle. Supporting cell and hair cell populations of chicken utricle obtained by laser capture microdissection, following to do RNA extraction and hybridization on Affymetrix microarrays.

2016-05-17 | E-GEOD-81461 | biostudies-arrayexpress

Embryonic day 15 chick utricle single cell analysis

Project description:Single-cell proteomics can reveal the changing protein composition of differentiating cells. We used shotgun mass spectrometry to determine the abundant proteins present in single or small pools of subpicoliter-sized cells from the embryonic day 15 (E15) utricle of the chicken inner ear, when many hair cells are differentiating from progenitor (supporting) cells. The actin monomer binding protein thymosin β4 (TMSB4X) was present in E15 progenitor cells at nearly equimolar levels relative to actin, but dropped to one-tenth that value in hair cells, with little change in total actin. Single-cell RNA-seq analysis of E15 utricle cells showed that TMSB4X transcripts fell in abundance once hair-cell differentiation initiated. These results suggest that most actin is sequestered in progenitor cells, but upon differentiation to hair cells, actin is released, permitting assembly of the sensory hair bundle.

2019-11-12 | PXD014256 | Pride

GATA3 siRNA in utricle sensory epithelia

Project description:The inner ear utilizes sensory hair cells as mechano-electric transducers for sensing sound and balance. In mammals, these hair cells lack the capacity for regeneration. Unlike mammals, hair cells from non-mammalian vertebrates, such as birds, can be regenerated throughout the life of the organism making them a useful model for studying inner ear genetics pathways. The zinc finger transcription factor GATA3 is required for inner ear development and mutations cause sensory neural deafness in humans. In the avian cochlea GATA3 is expressed throughout the sensory epithelia; however, expression is limited to the striola of the utricle. The striola corresponds to an abrupt change in morphologically distinct hair cell types and a 180Â° shift in hair cell orientation. We used 3 complimentary approaches to identify potential downstream targets of GATA3 in the avian utricle. Specifically we used microarray expression profiling of GATA3 knockdown by siRNA and GATA3 over-expression treatments as well as direct comparisons of GATA3 expressing cells from the striola and non GATA3 expressing cells from the extra-striola. Whole utricle specimens were treated with streptomycin for 24 hrs, rinsed and allowed to recover for an additional 24 hrs. Whole utricles were transfected with either GATA3 or GFP 21mer synthetic siRNAs for an additional 48 hrs and pure sensory epithelia were isolated. There are 2 biological samples and experiments include technical replicates as well as dye-switches for a total of 8 microarrays.

2010-06-24 | E-GEOD-14785 | biostudies-arrayexpress

Gallus gallus utricle striola vs. extra-striola

Project description:The inner ear utilizes sensory hair cells as mechano-electric transducers for sensing sound and balance. In mammals, these hair cells lack the capacity for regeneration. Unlike mammals, hair cells from non-mammalian vertebrates, such as birds, can be regenerated throughout the life of the organism making them a useful model for studying inner ear genetics pathways. The zinc finger transcription factor GATA3 is required for inner ear development and mutations cause sensory neural deafness in humans. In the avian cochlea GATA3 is expressed throughout the sensory epithelia; however, expression is limited to the striola of the utricle. The striola corresponds to an abrupt change in morphologically distinct hair cell types and a 180° shift in hair cell orientation. We used 3 complimentary approaches to identify potential downstream targets of GATA3 in the avian utricle. Specifically we used microarray expression profiling of GATA3 knockdown by siRNA and GATA3 over-expression treatments as well as direct comparisons of GATA3 expressing cells from the striola and non GATA3 expressing cells from the extra-striola. To identify genes that are co-expressed with GATA3 at the striola reversal zone, we compared gene expression in cells micro-dissected from the sensory epithelia of the chick utricle striola to cells from the surrounding extra-striola. There are 2 biological samples and experiments include technical replicates as well as dye-switches for a total of 8 microarrays.

2009-12-24 | E-GEOD-14783 | biostudies-arrayexpress

The Transcriptome of Utricle Hair Cell Regeneration in the Avian Inner Ear

Project description:A comprehensive transcriptome profile of chicken utricle hair cell across a 7 days regenerative time course.

2014-04-29 | GSE57134 | GEO