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Rat utricle hair bundles and whole utricles—LTQ

ABSTRACT: 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.

INSTRUMENT(S): LTQ

ORGANISM(S): Rattus Norvegicus (rat)

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

SUBMITTER: Peter Barr-Gillespie

LAB HEAD: Peter Barr-Gillespie

PROVIDER: PXD002416 | Pride | 2015-11-17

REPOSITORIES: Pride

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			Action	DRS
	CHI483_R1-1_20080826_LT.RAW	Raw
	CHI483_R1-2_20080826_LT.RAW	Raw
	CHI483_R1-3_20080826_LT.RAW	Raw
	PPG875_Rat1_20101013_LT.RAW	Raw
	PPG875_Rat2_20101013_LT.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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Mouse utricle hair bundles and whole utricles—Velos

Project description: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.

2015-11-17 | PXD002415 | Pride

Chick utricle hair bundles and utricular epithelium—LTQ

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 mass spectrometer for protein detection.

2015-11-17 | PXD002410 | Pride

Chick utricle hair bundles and utricular epithelium—Velos

2015-11-17 | PXD002414 | 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

Comparison of hair bundle proteomes from WT and Pls1-knockout mouse utricles

Project description:With their stereotyped dimensions and orderly arrangement, as well as their essential role in auditory and vestibular function, stereocilia of sensory hair cells provide a particularly prominent example of the importance of cellular actin protrusions. Uniformity of actin packing in stereocilia is mediated by actin crosslinkers of the plastin, fascin, and espin families. While mice lacking ESPN (espin) have no vestibular function, we found that mice that either lacked PLS1 (plastin 1) or had nonfunctional FSCN2 (fascin 2) had vestibular function that was modestly reduced, with double-mutant mice being more strongly affected. Despite its outsized importance in functional assays, targeted mass spectrometry indicated that ESPN only accounted for ~15% of the total crosslinkers in mouse utricle stereocilia. PLS1 was the most abundant of the crosslinkers, and the second-most-abundant protein overall in stereocilia. Stereocilia lacking PLS1 were shorter and thinner than wild-type stereocilia. Surprisingly, while wild-type stereocilia had random liquid packing of their actin filaments, stereocilia lacking PLS1 had orderly hexagonal packing. Stereocilia with normal PLS1 but that lacked functional FSCN2 had normal liquid packing and normal dimensions. All three crosslinkers are required for normal stereocilia structure and function, but PLS1 biases stereocilia towards liquid packing, which allows stereocilia to grow to greater diameter.

2016-09-28 | PXD004044 | Pride

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

Mouse wild-type and Anxa5-null utricles and hair bundles

Project description:The phospholipid- and Ca2+-binding protein annexin A5 (ANXA5) is the most abundant membrane-associated protein of ~P23 mouse vestibular hair bundles, present at ~15,000 copies per stereocilium, which is ~2% of the total protein there. Although seven other annexin genes are expressed in mouse utricles, mass spectrometry showed that none were upregulated in stereocilia of Anxa5-/- mice. Annexins have been proposed to mediate Ca2+-dependent repair of membrane lesions, which could be part of the repair mechanism in hair cells after noise damage. Nevertheless, Anxa5-/- mice not only have normal hearing or balance, but are identical to wild-type mice in their temporary or permanent hearing changes following noise exposure. We suggest that the significant amounts of ANXA2 and ANXA6 that are present in the hair-cell cytoplasm can substitute in any function carried out by ANXA5, and that ANXA5 may be playing a hitchhiker role in the bundle. These results demonstrate that abundance of a protein in a specific compartment or cellular structure does not necessarily imply functional significance.

2016-06-09 | PXD003005 | Pride

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

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