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Chick utricle hair bundles and utricular epithelium—Velos

ABSTRACT: 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.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Gallus Gallus (chicken)

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

SUBMITTER: Peter Barr-Gillespie

LAB HEAD: Peter Barr-Gillespie

PROVIDER: PXD002414 | Pride | 2015-11-17

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	Chick_Velos_FASTA.zip	Other
	Chick_Velos_ThresholdFigures_BUN.zip	Other
	Chick_Velos_ThresholdFigures_UTR.zip	Other
	Chick_Velos_filtered_SQT.zip	Other
	Chick_Velos_miscellaneous.zip	Other

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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

Similar Datasets

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

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

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

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.

2015-11-17 | PXD002416 | Pride

The Proteome of Mouse Vestibular Hair Bundles Over Development

Project description:Development of the vertebrate hair bundle is a precisely orchestrated event that culminates in production of a tightly ordered arrangement of actin-rich stereocilia and a single axonemal kinocilium. To understand how the protein composition of the bundle changes during development, we isolated bundles from young (postnatal days P4-P6) and mature (P21-P25) mouse utricles using the twist-off method, then characterized their constituent proteins using liquid-chromatography tandem mass spectrometry with data-dependent acquisition. Using label-free quantitation, we measured relative abundances of proteins in both bundles and in the whole utricular epithelium; comparison of protein abundance between the two fractions allows calculation of enrichment in bundles. These data will be useful for examining the proteins present in mammalian vestibular bundles and how they change over development.

2015-08-17 | PXD002167 | Pride

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

Immunologic pathways in protective versus maladaptive host responses to attenuated and pathogenic strains of Mycoplasma gallisepticum

Project description:The goal of this study was to compare the host's response (chicken tracheal epithelium) to laboratory attenuated vaccine versus pathogenic strains of M. gallisepticum

2019-02-20 | E-MTAB-7675 | biostudies-arrayexpress

D10 Stereocilia Membrane Enrichment

Project description:Through its activity in stereocilia, MYO7A (myosin VIIA) is essential for hair cell function in the inner ear. Utilizing multiple stages of immunoaffinity enrichment, we have developed a strategy that allows us to partially purify stereocilia membranes from thousands of chick inner ears and isolate low-abundance MYO7A protein complexes from those membranes. The D10 stereocilia membrane enrichment protocol involves density centrifugation steps and immuno-enrichment of stereocilia using the D10 antibody, directed against the major stereocilia transmembrane protein PTPRQ. The data in this submission document the effectiveness of the enrichment procedure.

2016-08-16 | PXD004222 | Pride

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