Sensory epithelia of cochlear explant
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ABSTRACT:
PROVIDER: PRJNA1031790 | ENA |
REPOSITORIES: ENA
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Project description:To understand the molecular control of development and regeneration in the mammalian cochlear sensory epithelia, we performed a comparative study of gene expression patterns between postnatal day-3 (P3) and adult stages using a microarrays approach. Two inner ear development stages were used in this study, Post-natal day three and eight-week-old adult. A total number of sixty Swiss mice were exploited for each stage. The cochlear sensory epithelia (CSE) were collected from the inner ears and immediately placed in RNA later solution. A total of six independent dissection experiments were carried out separately in order to obtain three biological replicates for each stage. In each experiment, the CSE from 20 mice were pooled. Total RNA was purified from each biological sample separately using RNAeasy Mini Kit and the RNA integrity was assessed by the Nanodrop 2000
2012-01-01 | E-GEOD-32963 | biostudies-arrayexpress
Project description:To understand the molecular control of development and regeneration in the mammalian cochlear sensory epithelia, we performed a comparative study of gene expression patterns between postnatal day-3 (P3) and adult stages using a microarrays approach.
2012-01-01 | GSE32963 | GEO
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. 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
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. Dissociated sensory epithelia were plated in 96 well cultures, 5 wells per sample. 4 days post plating, ~ 30% confluency, cells were transfected with a pMES vector containing an internal ribosome entry site regulating expression of GATA3 and eGFP under control of a chick beta-actin promoter. Controls were transfected with a vector containing EGFP only. 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-14784 | biostudies-arrayexpress
Project description:We have employed a novel approach for the identification of functionally important microRNA (miRNA)-target interactions using integrated miRNA, transcriptome and proteome profiles with advanced in silico analysis. By looking at both the transcript and protein levels of expression, a thorough coverage of miRNA regulation was obtained. Microdissected auditory and vestibular sensory epithelia were used as the model system, thus being the first time such a comparison was carried out in a neuroepithelial system. Moreover, this is one of only a few studies employing proteome screening for the identification of miRNA targets. Notably, this approach can be employed for the study of other tissues and organs. We detected the expression of 157 miRNAs in the inner ear sensory epithelia, with 53 miRNAs differentially expressed between the cochlea and vestibule. By searching for enrichment and depletion of miRNA targets in the transcript and protein datasets with a reciprocal or similar expression, respectively, as the regulatory miRNA, we identified functionally important miRNAs. Finally, the interaction between miR-135b and PSIP1-P75, a transcriptional coacitvator previously unknown in the inner ear, was identified and validated experimentally. We suggest that miR-135b may serve as a cellular effector, involved in regulating some of the differences between the cochlear and vestibular hair cells. We investigated the mRNA expression profile of the cochlear and vestibular sensory epithelia from inner ears of postnatal day 2 mice using the Affymetrix GeneChip® 430 2Mouse Genome array. Cochlear and vestibular sensory epithelia were dissected from wild type C3H mice and collected separately. The vestibular epithelia consisted of the saccule, utricle and the lateral and anterior cristae. Both the cochlear and vestibular sensory epithelia were dissected with their underlying mesenchyma. Altogether three pools, three biological replicates, of each tissue type were collected consisting of cochlear or vestibular sensory epithelia dissected from 10 to 12 inner ears.
2011-04-20 | E-GEOD-23081 | biostudies-arrayexpress
Project description:The inner ear utilizes sensory hair cells as mechano-electric transducers for sensing sound and balance. In mammals, these sensory hair cells lack the capacity for regeneration and if damaged lead to hearing or balance disorders. However, non-mammalian vertebrates such as birds maintain their regenerative abilities throughout their life. In a previous study we conducted a gene expression profiling time course of regenerating sensory epithelia (SE) in avian cochlea and utricle on a custom transcription factor microarray following damage by both laser and chemical ablation. We identified several known signaling cascades such as The Pax-Eya-Six-Dach pathway, Ap-1 pathway, the Tgf-β pathway and sonic hedgehog signaling that are differentially expressed during SE regeneration. In this study we selected 27 of these genes for knockdown by siRNA or small molecule inhibition to determine their requirement for SE regeneration and identify downstream targets. We assessed phenotypes using a 96 well proliferation assay and expression profiled each knockdown on a custom transcription factor microarray. Using these techniques we have determined several genes that are required for SE proliferation and identified novel epistatic relationships between many of these genes. Pure sensory epithelia was isolated from avian utricles. Sensory epithelia was physically dissociated and grown in 96 well cultures for 3 days. Prior to confluency, dissociated sensory epithelia were transfected with siRNAs (12 pmol/well) or small molecule inhibitor in 0.1% DMSO. RNA was isolated 24 hrs post transfection and assayed on a custom oligonucleotide transcription factor microarray compared to controls (GFP siRNA or 0.1% DMSO only). siRNA: CEBPG, JunD, BTAF1, LRP5, PAX2, PAX5, PAX7, Wnt4, BCL11A, CBX3, CBX4, CTNNB1, CUTL1, MYT1L, RARA, TIMELESS, TRIP15, PAX3, EZH2, HES1, ID1, CDKN1B, and PPARGC1 small molecule inhibition: IGF, MAPK, SHH, and JNK
2010-07-02 | E-GEOD-16842 | biostudies-arrayexpress
Project description:In the inner ear, cochlear and vestibular sensory epithelia utilize grossly similar cell types to transduce different stimuli: sound and acceleration. Each individual sensory epithelium is composed of highly heterogeneous populations of cells based on physiological and anatomical criteria. However, limited numbers of each cell type have impeded transcriptional characterization. Here we generated transcriptomes for 301 single cells from the utricular and cochlear sensory epithelia of newborn mice to circumvent this challenge. Cluster analysis indicates distinct profiles for each of the major sensory epithelial cell types, as well as less distinct subpopulations. Asynchrony within utricles allows reconstruction of the temporal progression of cell-type specific differentiation and suggests possible plasticity among cells at the sensory-nonsensory boundary. Comparisons of cell types from utricles and cochleae demonstrate divergence between auditory and vestibular cells despite a common origin. These results provide significant insights into the developmental processes that form unique inner ear cell types.
2015-10-15 | GSE71982 | GEO
Project description:Regenerating hair cells in human vestibular sensory epithelia
| PRJNA430413 | ENA
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.
2009-12-25 | GSE14785 | GEO
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.
2009-12-25 | GSE14784 | GEO