Gene expression profile of cells from cochlear organoids and comparison with in vivo auditory sensory epithelium cells.
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ABSTRACT:
PROVIDER: PRJNA748693 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15207941_1.fastq.gz | Fastqsanger.gz | |||
| SRR15207941_2.fastq.gz | Fastqsanger.gz | |||
| SRR15207942_1.fastq.gz | Fastqsanger.gz | |||
| SRR15207942_2.fastq.gz | Fastqsanger.gz | |||
| SRR15207943_1.fastq.gz | Fastqsanger.gz |
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Project description:We sequenced the total RNA of cells from inner ear organoids generated by EFI,EFI-4C and EFI-CL expansion strategies. Transcriptional profiles revealed that CHIR and LPA significantly increased proliferative potency and contributed to the stemness maintenance. We further compared the gene expression profiles among the sorted Lgr5+ CPCs, the primary organoids of passage (P)0, the P4 organoids, and the sorted E-cadherin+ sensory epithelial cells. Inner ear organoids recapitulated genetic characteristics of auditory epithelium rather than Lgr5+ progenitors alone. Differential gene analysis of cells from primary organoids and organoids at fourth passage indicated stable transcriptional profiles among passages, which confirmed the reliability and authenticity of cochlear organoids for modeling the properties of the cochlea.
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Project description:The mouse cochlear sensory epithelium proteome has been characterized using FASP combined with GELFrEE and off-line SCX- and WAX-based methods follwed by nano LC-MS/MS. In addition, we utilzed single digestion and double digestion approaches using LysC and trypsin endoproteases. MS data files were processed with MaxQuant (Version 1.2.2.5, Max Planck Institute) and peak list files were searched by MASCOT search engine against the UniProt mouse database containing both forward and reversed protein sequences and common contaminants such as keratin. The initial parent and fragment ion maximum precursors were set to 6 ppm and 0.5 Da, respectively. The search included a fixed modification of carbamidomethyl of cysteine and variable modifications of oxidation of methionine and protein N-terminal acetylation. The minimum peptide length to be considered for identification was 6 amino acids.
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Project description:Inner ear cochlear supporting cells (SCs) are highly specialized glia-like cells that structurally and functionally support neighboring mechano-sensory hair cells. Despite their importance for proper auditory function, little is known about the molecular mechanisms that control their development. In this study we investigated the function of the Notch ligand Jagged1 (Jag1) in cochlear SC differentiation and maintenance. To address the function of Jag1 in the differentiation of SCs, we conditionally deleted Jag1 in stage E14.5 SC precursors using the recently established Sox2-CreER/+ and Jag1 fx/fx mouse lines. Analysis of stage P0 Jag1 mutant and control animals revealed that Hensen cells, a highly specialized SC-subtype located at the lateral edge of the auditory sensory epithelium, failed to form in the absence of Jag1. Other SC-subtypes did form in the absence of Jag1, however, their morphology and cellular arrangement was abnormal and SC-subtype specific genes and genes associated with mitochondrial function and protein synthesis were significantly reduced, indicating global defects in SC differentiation and SC homeostasis.
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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.
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Project description:As the primary sensory neurons of the auditory system, Type I spiral ganglion neurons (SGNs) encode sound stimulus properties critical for the formation of auditory percept in higher brain areas. Their functional heterogeneity is thought to contribute to our ability to hear a wide range of sound intensities and against background noise, but how SGN diversity arises during development is poorly understood. Here we studied the role of the transcription factor Runx1 in establishing SGN heterogeneity in the mouse cochlea by single cell RNA-sequencing.
2023-01-13 | GSE210216 | GEO
Project description:As the primary sensory neurons of the auditory system, Type I spiral ganglion neurons (SGNs) encode sound stimulus properties critical for the formation of auditory percept in higher brain areas. Their functional heterogeneity is thought to contribute to our ability to hear a wide range of sound intensities and against background noise, but how SGN diversity arises during development is poorly understood. Here we studied the role of the transcription factor Runx1 in establishing SGN heterogeneity in the mouse cochlea by single cell RNA-sequencing.
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Project description:Runx1 Controls Auditory Sensory Neuron Diversity (iCKO)
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Project description:Runx1 Controls Auditory Sensory Neuron Diversity (CKO)
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Project description:The cochlear nucleus is the first central pathway involved in the processing of peripheral auditory activity. It is heterogeneous in neuronal populations and physiologic responses and is organized in three major subdivisions: the anterior ventral cochlear nucleus (AVCN), the posterior ventral cochlear nucleus (PVCN) and the dorsal cochlear nucleus (DCN). Although each region demonstrates multiple cell types and functions, there are predominant populations of neurons in each region that underlie the principal role each subdivision plays in auditory processing. Little is known of the underlying genetic contribution to these properties. This study sought to identify genes expressed in the subdivisions of the cochlear nucleus that may account for the anatomical and physiological characteristics of each subdivision. These data provide a genetic basis for understanding normal auditory processing in the cochlear nucleus and a template for investigating changes that may occur with hearing loss, the generation and percept of tinnitus, and central processing disorders. Keywords: normal, comparative Brown Norway rats (n=40, female, 45days) were anesthetized and decapitated. Brains were rapidly removed and the subdivisions of the cochlear nucleus (AVCN, PVCN and DCN) dissected on dry ice. Total RNA was extracted and tested for concentration and purity by spectrophotometry and integrity by gel electrophoresis. SAGE was performed using the NlaIII enzyme and Invitrogen SAGE kit. Concatemers were commercially sequenced and imported into eSAGE (Margulies and Innis, 2000) for tag extraction and frequency.
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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
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