Exhaustive screening of outer hair cell-specific genes
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ABSTRACT:
PROVIDER: PRJNA497334 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mechanosensory outer hair cells (OHC) play an essential role in the amplification of sound-induced vibrations in the cochlea because of their ability to contract or elongate following changes in the intracellular potential. To study the critical roles of OHC, we generated a novel mouse model, OHC-TRECK, for hearing impairment by introducing the human diphtheria toxin (DT) receptor gene under the control of the OHC-specific promoter of the mouse prestin gene. DT administration to OHC-TRECK mice resulted in severe hearing impairment with a decrease in the amplitude of distortion product otoacoustic emissions and elevated auditory brainstem responses. We performed a differential expression analysis between DT-administered OHC-TRECK and wild-type mice using high-throughput microarray analysis to screen for novel, specifically expressed and functional genes involved in the development and maintenance of OHC.
2019-04-09 | GSE121442 | GEO
Project description:In order to determine the regulators of outer hair cell postnatal maturation, we utilized the RiboTag mouse model to perform a detailed transcriptomic analysis of outer hair cells at five postnatal developmental time points: P8, P14, P28, 6 weeks (6wk) and 10 weeks (10wk). This analysis resulted in consistent enrichment of outer hair cell expressed genes in the immunoprecipitated RNA compared to whole cochlear input RNA from each time point. Using transcription factor binding motif prediction on a set of defined outer hair cell enriched genes, we further use this dataset to identify the helios transcription factor as a regulator of the postnatal outer hair cell transcriptome.
2018-11-28 | GSE116703 | GEO
Project description: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.
2018-08-02 | GSE111348 | GEO
Project description:Exhaustive screening of outer hair cell-specific genes
| PRJDB3602 | ENA
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
Project description:RiboTag translatome analysis of outer hair cell postnatal development
| PRJNA479956 | ENA
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.
2014-08-12 | GSE56866 | GEO
Project description:RNA-sequencing of Adult Mouse Inner Hair Cells and Outer Hair Cells of the organ of Corti
| PRJNA436761 | ENA
Project description:Next Generation Sequencing (NGS) based mRNA sequencing (RNA-seq) has provided high-throughput measurements to analyze the transcriptome of cells. We report the comprehensive transcriptome profiling of primarily isolated human mesenchymal stem cells from hair follicle outer root sheath (MSCORS) in series cultivation passages using NGS-based RNA-seq method. Human anagen hair follicles were non-invasively plucked from scalp of healthy donors, cultivated on a Transwell membrane, from which the MSCORS were isolated and subcultured onto normal culture flask. Attached and proliferating MSCORS were cultivated and characterized as mesenchymal stem cells (MSC) according to the minimum criteria for defining multipotent MSC from the International Society for Cellular Therapy (ISCT). mRNA profiles of MSCORS in p0, p1 and p2 were quality controlled, and generated by deep sequencing, in triplicate, using Illumina PE150. Paired-end raw data were pre-processed using a published protocol. HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align reference genome. HTSeq was used to calculate Reads Count, and gene abundence was determined by analyzing FPKM (fragments per kilobase of exon model per million reads mapped).
2020-10-07 | GSE159139 | GEO
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