Similar Datasets
Project description:Inner-ear miRNA Time-course Expression
| PRJNA429755 | ENA
Project description:The inner ear sensory neurons play a pivotal role in auditory processing and balance control. Though significant progresses have been made, the underlying mechanisms controlling the differentiation and survival of the inner ear sensory neurons remain largely unknown. During development, ISL1 and POU4F transcription factors are co-expressed and are required for terminal differentiation, pathfinding, axon outgrowth and the survival of neurons in the central and peripheral nervous systems. However, little is understood about their functional relationship and regulatory mechanism in neural development. Here, we have knocked out Isl1 or Pou4f1 or both in mice of both sexes. In the absence of Isl1, the differentiation of cochleovestibular ganglion (CVG) neurons is disturbed and with that Isl1-deficient CVG neurons display defects in migration and axon pathfinding. Compound deletion of Isl1 and Pou4f1 causes a delay in CVG differentiation and results in a more severe CVG defect with a loss of nearly all of spiral ganglion neurons (SGNs). Moreover, ISL1 and POU4F1 interact directly in developing CVG neurons and act cooperatively as well as independently in regulating the expression of unique sets of CVG-specific genes crucial for CVG development and survival by binding to the cis-regulatory elements including the promoters of Fgf10, Pou4f2, and Epha5 and enhancers of Eya1 and Ntng2 These findings demonstrate that Isl1 and Pou4f1 are indispensable for CVG development and maintenance by acting epistatically to regulate genes essential for CVG development.
2024-05-31 | GSE233706 | GEO
Project description:The morphogenesis of the otic vesicle (OV) to form inner ear organs serves as an excellent model system to understand cell fate acquisition on a single cell level. Tbx2 and Tbx3 (Tbx2/3) encode closely related T-box transcription factors that are expressed widely in the mammalian otic vesicle (OV). Inactivation of both genes in the Pax2-Cre lineage (Tbx2/3cKO) results in failed morphogenesis of the OV into inner ear organs. To understand the basis of these defects, single cell RNA-sequencing (scRNA-seq) was performed on the OV lineage using Pax2-Cre, in controls versus Tbx2/3cKO embryos, at stage E10.5. We identified a multipotent population termed otic progenitors that are localized to the anterior ventrolateral region of the OV in controls and are marked by expression of Fgf18, Sox3, and Cxcl12. The otic progenitor population was increased three-fold in Tbx2/3cKO embryos, concomitant with dysregulation of genes in these cells as well as reduced progression to more differentiated states of prosensory and nonsensory cells. An ectopic neural population of cells was detected in the posterior OV of Tbx2/3cKO embryos due to increased expression of Neurog1 and NeuroD1 but with reduced maturation. As all three cell fates were affected in Tbx2/3cKO embryos, we suggest that Tbx2/3 promotes progression of multipotent otic progenitors to more differentiated cell types in the OV.
2022-12-12 | GSE185172 | GEO
Project description:Isl1 and Pou4f1 regulate a unique set of CVG gene cooperatively or individually. GO term analysis shows these genes are crucial for CVGs development. To estimate Isl1 and Pou4f1 directly or indirectly regulate these downstream genes and how they act to affect these genes, we performed the CUT&Tag of ISL1 and POU4F1 with the histone modifications, H3K4me3, H3K27ac and H3K27me3 in CVGs. The identity of the peaks were characterized and big chromatin profiles were obtained.
2024-05-31 | GSE233840 | GEO
Project description:The correlation between expression levels of mRNA and protein in mammals is relatively low, with a Pearson correlation coefficient of ~0.40. Post transcriptional regulation contributes to this low correlation. Across taxa, it was demonstrated that translation efficiency, i.e. the protein-to-mRNA ratio in steady state, varies between species in a direction that buffers the protein levels from changes in the transcript abundance. Evidence for this behavior in tissues is sparse. We asked whether this phenomenon is evident in our auditory system data, and on previously obtained proteomic and transcriptomic data from different tissue datasets.
2017-04-24 | PXD003379 | Pride
Project description:MPSS analysis of signatures from microdissections of mouse inner ear tissues. Keywords: other
2006-10-01 | GSE4965 | GEO
Project description:We report the application of single cell RNA sequencing for determining cell type and quantity in developing inner ear organoids derived from human pluripotent stem cells. By obtaining samples from multiple time points throughout differentiation, we developed a roadmap at single cell resolution of the multiple cell lineages which give rise to in vitro inner ear tissue as well as 'off-target' tissue types. We find that the cells in the day 0 sample contained primarily a homogenous population of pluripotent stem cells. On day 3, after treatment with BMP4, we find that the cells have differentiated into a split between surface ectoderm, the progenitor of the inner ear tissue, and neuroectoderm. On day 6 and 8, we observed the emergence of cranial placode tissue, both anterior and posterior. Then, after treatment starting on day 8 with a WNT agonist, CHIR, we observed the maturation of inner ear tissue into hair cells and neurons, starting on day 18 and increasing through the last time point collected, day 36. This study provides an atlas of inner ear organoid differentiation from human pluripotent stem cells.
2021-11-23 | GSE188936 | GEO
Project description:The inner ear continues to grow and develop until the auditory and vestibular systems reach full maturity and all of the genes involved in this process have yet to be identified. Previous gene based analysis have primarily focused on the early developmental stages following induction and initial formation of the inner ear. The aim of this study is to identify new candidate genes for inner ear development. Microarrays were used to produce expression profiles from larval stages 56,57,58 of the Xenopus laevis inner ear. The data produced from this work represent an annotated resource that can be utilized by the Xenopus community to provide candidates for further functional analysis. Xenopus inner ears were isolated from larval animals for RNA extraction and hybridization to Affymetrix GeneChip microarrays.
2016-02-29 | E-GEOD-73829 | biostudies-arrayexpress
Project description:A forward genetic screen of N-ethyl-N-nitrosourea mutagenized Xenopus tropicalis has identified an inner ear mutant named eclipse (ecl). Mutants developed enlarged otic vesicles and various defects of otoconia development; they also showed abnormal circular and inverted swimming patterns. Positional cloning identified specificity protein 8 (sp8), which was previously found to regulate limb and brain development. Two different loss-of-function approaches using transcription activator-like effector nucleases and morpholino oligonucleotides confirmed that the ecl mutant phenotype is caused by down-regulation of sp8. Depletion of sp8 resulted in otic dysmorphogenesis, such as uncompartmentalized and enlarged otic vesicles, epithelial dilation with abnormal sensory end organs. When overexpressed, sp8 was sufficient to induce ectopic otic vesicles possessing sensory hair cells, neurofilament innervation in a thickened sensory epithelium, and otoconia, all of which are found in the endogenous otic vesicle. We propose that sp8 is an important factor for initiation and elaboration of inner ear development.
| S-EPMC4035935 | biostudies-literature
Project description:The inner ear continues to grow and develop until the auditory and vestibular systems reach full maturity and all of the genes involved in this process have yet to be identified. Previous gene based analysis have primarily focused on the early developmental stages following induction and initial formation of the inner ear. The aim of this study is to identify new candidate genes for inner ear development. Microarrays were used to produce expression profiles from larval stages 50,51,52 of the Xenopus laevis inner ear. The data produced from this work represent an annotated resource that can be utilized by the Xenopus community to provide candidates for further functional analysis.
2016-12-31 | GSE73828 | GEO