Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-sequencing of Adult Mouse Inner Hair Cells and Outer Hair Cells of the organ of Corti

ABSTRACT: To further understand the biological properties of hair cells of the mammalian cochlea, we examined the transcriptome of adult inner and outer hair cells. Morphologically distinct inner and outer hair cells were isolated from the organ of Corti from adult CBA/J mice. One thousand inner and outer hair cells were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of two biological replicates of IHCs and three biological replicates of OHCs, each with two technical repeats, was performed. The resulting sequenced reads were mapped. Comparisons between inner and outer hair cells allow identification of enriched genes, as well as differentially expressed genes that result in cellular specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult mouse inner and outer hair cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE111348 | GEO | 2018/08/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomes of the Cochlear Inner and Outer Hair Cells

Project description:The transcriptome is the complete set of all RNA transcripts produced by the genome in a cell and reflects the genes that are being actively expressed. Transcriptome analysis is essential for understanding the genetic mechanism controlling the phenotype of a cell. Using DNA microarray technique we examined transcriptomes of 2,000 individually collected inner (IHCs) and outer hair cells (OHCs), two types of auditory sensory cells critical for hearing. Among approximately 16,645 and 17,711 transcripts considered to be expressed, 1,296 and 256 genes showed significant differential expression in IHCs and OHCs, respectively. The top ten differentially expressed genes include Slc17a8, Dnajc5b, Slc1a3, Atp2a3, Osbpl6, Slc7a14, Bcl2, Bin1, Prkd1, Map4k4 in IHCs, and Slc26a5, C1ql1, Strc, Dnm3, Plbd1, Lbh, Olfm1, Plce1, Tectb, Ankrd22 in OHCs. Many unknown sequences and non-coding RNAs were also expressed in hair cells. The differentially expressed genes underlie the genetic mechanism for unique functions of IHCs and OHCs. The total RNA was extracted from the collected pools of single outer hair cell (OHC) and inner hair cell (IHC). Their whole-genome transcriptome expression was detected using GeneChip microarray analysis. The analysis and comparison between OHC and IHC allow us to determine what genes are expressed and what genes are uniquely or differential expressed in each population.

2014-08-12 | E-GEOD-56866 | biostudies-arrayexpress

Transcriptomes of the Cochlear Inner and Outer Hair Cells

2014-08-12 | GSE56866 | GEO

Development and transdifferentiation into inner hair cells require Tbx2

Project description:Atoh1 is essential for the development of both outer hair cells (OHCs) and inner hair cells (IHCs) in the mammalian cochlea. Whereas Ikzf2 is necessary for OHC development, the key gene required for IHC development remains unknown. We found that deletion of Tbx2 in neonatal IHCs led to their transdifferentiation into OHCs by repressing 26.7% of IHC genes and inducing 56.3% of OHC genes, including Ikzf2. More importantly, persistent expression of Tbx2 coupled with transient Atoh1 expression effectively reprogramed non-sensory supporting cells into new IHCs expressing the functional IHC marker vGlut3. The differentiation status of these new IHCs was considerably more advanced than that previously reported. Thus, Tbx2 is essential for IHC development, and co-upregulation of Tbx2 with Atoh1 in supporting cells represents a new approach for treating deafness related to IHC degeneration.

2022-08-09 | GSE199369 | GEO

Dual expression of Atoh1 and Ikzf2 promotes transformation of adult cochlear supporting cells into outer hair cells

Project description:Mammalian cochlear outer hair cells (OHCs) are essential for hearing. Severe hearing impairment follows OHC degeneration. Previous attempts at regenerating new OHCs from cochlear supporting cells (SCs) have been unsuccessful, notably lacking expression of the key OHC motor protein, Prestin. Thus, regeneration of Prestin+ OHCs represented a barrier to restoring auditory function in vivo. Here, we reported the successful in vivo conversion of adult mouse cochlear SCs into Prestin+ OHC-like cells through the concurrent induction of two key transcriptional factors known to be necessary for OHC development: Atoh1 and Ikzf2. Single cell RNA sequencing reveals the upregulation of 729 OHC genes and downregulation of 331 SC genes in OHC-like cells. The resulting differentiation status of these OHC-like cells was much more advanced than previously achieved. This study thus established an efficient approach to induce the regeneration of Prestin+ OHCs, paving the way for in vivo cochlear repair via SC transdifferentiation.

2021-09-03 | GSE161156 | GEO

RNA-sequencing of Adult Mouse Inner Hair Cells and Outer Hair Cells of the organ of Corti

Project description:RNA-sequencing of Adult Mouse Inner Hair Cells and Outer Hair Cells of the organ of Corti

| PRJNA436761 | ENA

Mass spectrometry identification of proteins of isolated auditory and vestibular hair cells using data-independent and data-dependent acquisition

Project description:Hair cells undergo postnatal development that leads to formation of their sensory organelles, synaptic machinery, and in the case of cochlear outer hair cells, their electromotile mechanism. To examine the proteome changes over development, we isolated pools of 5000 Pou4f3-Gfp positive or negative cells from the cochlea or utricles; these cell pools were analyzed by data-dependent and data-independent acquisition (DDA and DIA) mass spectrometry. DDA data were used to generate spectral libraries, which enabled identification and accurate quantitation of specific proteins using the DIA datasets. We also isolated and pooled individual inner and outer hair cells from adult cochlea and compared their proteomes to those of developing hair cells. The DDA and DIA datasets will be valuable for accurately quantifying proteins in hair cells and non-hair cells over this developmental window.

2017-09-18 | PXD006240 | Pride

In situ regeneration of inner hair cells in the damaged cochlea by temporally regulated coexpression of Atoh1 and Tbx2

Project description:Cochlear inner hair cells (IHCs) are primary sound receptors, and thus in efforts to develop treatments for hearing impairment. IHC regeneration in vivo has been widely attempted, although not yet in the IHC-damaged cochlea. Moreover, the extent to which new IHCs resemble wild-type IHCs remains unclear, as does whether new IHCs can yield hearing improvement. Here, we developed an in vivo mouse model wherein wild-type IHCs were pre-damaged and nonsensory supporting cells were transformed into IHCs by ectopically expressing Atoh1 transiently and Tbx2 permanently. Notably, the new IHCs expressed the functional marker vGlut3 and presented similar transcriptomic and electrophysiological properties as wild-type IHCs. Furthermore, the formation efficiency and maturity of new IHCs were higher than those previously reported, although marked hearing improvement was not achieved, at least partly due to defective mechanoelectrical transduction (MET) in new IHCs. Thus, we successfully regenerated new IHCs resembling wild-type IHCs in multiple aspects in the damaged cochlea. Our findings suggest that the defective MET is a critical barrier preventing the restoration of hearing capacity and should thus facilitate future IHC regeneration studies.

2023-11-05 | GSE188259 | GEO

RNA-sequencing of Adult Zebrafish Inner Ear Hair Cells

Project description:To understand the basic biological properties of inner ear hair cells (HCs) from non-mammalian vertebrates, we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP-labeled HCs were isolated from inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. One thousand HCs and 1,000 non-sensory surrounding cells (nsSCs) were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs, which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution.

2017-11-18 | GSE101693 | GEO

Spontaneous firing activity in pre-hearing inner hair cells regulates the maturation of the mechanoelectrical transducer apparatus over a critical time-period

Project description:Sensory-independent Ca2+ spiking activity is crucial for the development of mammalian sensory systems. In the cochlea, spontaneous Ca2+ action potentials (APs) are present in the pre-hearing inner hair cells (IHCs), the frequency and pattern of which is modulated by ATP-dependent intercellular Ca2+ waves in the non-sensory cells. It remains unknown whether both these Ca2+-dependent signalling mechanisms in the cochlea are required for the functional maturation of the IHCs. We found that the intrinsic Ca2+ AP activity, but not that triggered by Ca2+ signalling in the non-sensory cells, regulates the maturation and maintenance of the stereociliary hair bundle in IHCs. We used a mouse model in which the potassium channel Kir2.1 is reversibly overexpressed in IHCs in vivo. Kir2.1 overexpression (Kir2.1-OE mice) prevented spontaneous Ca2+ spikes in IHCs, but not their modulation by ATP-induced signalling from non-sensory cells. Without spontaneous Ca2+ APs, mechanoelectrical transduction in IHCs disappeared prior the onset of hearing at P12 due to the progressive loss of stereocilia and their fusion. RNA-sequencing data showed that several pathways, including those involved in morphogenesis, actin-filament based processes, and Rho-GTPase signalling, were upregulated during the second postnatal week. By manipulating the in vivo expression of Kir2.1 channels, we identified the second post-natal week as the “critical point” after which spontaneous Ca2+ APs are required for proper hair bundle maintenance. We showed that the final stage of IHC maturation is finely regulated by their intrinsic electrical activity just before sound-induced sensory driven activity.

2023-01-01 | GSE215951 | GEO

Molecular changes associated with biological aging of cochlear hair cells

Project description:Age-related hearing loss (ARHL) is a progressive sensorineural hearing loss that occurs as people get older. As many as 35% to 50% of the population aged between 65 and 75 have ARHL. Although age-related changes in the central auditory system can contribute to hearing impairment, degeneration of the mechanosensitive hair cells in the cochlea is the prevalent cause of ARHL. The molecular mechanisms of hair cell aging are largely unknown. To provide a comprehensive dataset of age-related genes and pathways in hair cells, we individually collected inner and outer hair cells, the two types of sensory receptor cells in the cochlea, from 9- and 26-month-old CBA/J mice and performed cell type-specific transcriptomic analysis. Our analysis showed a significant reduction of the expression of genes related to hair cell structure and function such as Tmc1, Kcnq4, Kcnj13, Slc7a14, Slc17a8, Chrna9/Chrna10, and Slc26a5. Our hair cell-specific transcriptome analysis provides a rich resource for mechanistic studies of biological aging of cochlear hair cells.

2022-03-01 | GSE153882 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data