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 Zebrafish Inner Ear Hair Cells

ABSTRACT: 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.

ORGANISM(S): Danio rerio

PROVIDER: GSE101693 | GEO | 2017/11/18

SECONDARY ACCESSION(S): PRJNA395227

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells

Project description:To understand the basic biological property of hair cells (HCs) from lower vertebrates, we examined transcriptomes of adult zebrafish HCs. GFP-labeled HCs were isolated from the utricle, saccule, and lagena, the three inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. 2,000 HCs and 2,000 non-sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped, analyzed, and compared. Comparisons allow us to identify enriched genes in HCs, which may underlie HC specialization.

2018-02-06 | GSE92559 | GEO

Inner ear hair cell proteome

Project description:The mammalian inner ear subserves auditory and vestibular sensations via highly specialized cells and proteins. We show that sensory hair cells (HCs) employ hundreds of uniquely or highly expressed proteins for processes involved in transducing mechanical inputs, stimulating sensory neurons, and maintaining structure and function of these post-mitotic cells. Our proteomic analysis of purified HCs extends the existing HC transcriptome, revealing undetected gene products and isoform-specific protein expression. Comparison with mouse and human databases of genetic auditory/vestibular impairments confirms the critical role of the HC proteome for normal inner ear function, providing a cell-specific pool of candidates for novel, important HC genes. Several proteins identified exclusively in HCs by proteomics and by immunohistochemistry map to human genetic deafness loci, potentially representing new deafness genes.

2016-05-23 | MSV000079756 | MassIVE

Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids

Project description:The role of TMPRSS3 in hair cell (HC) remains unclear. Nelson and colleagues generated stem cell-derived inner ear organoids with Tmprss3-mutations to show that 1) inner ear organoids exhibit comparative effects of the genetic abnormality to its in vivo counterparts, 2) Tmprss3-mutations lead to apoptosis and reduced BK channels in HCs, and 3) cell membrane-bound TMPRSS3 is localized in HCs.

2019-05-31 | GSE130649 | GEO

Expression data from Pou4f3-Rb1 cKO and control inner ear

Project description:Retinoblastoma gene (Rb1) is required for proper cell cycle exit in the developing mouse inner ear and its deletion in the embryo leads to proliferation of sensory progenitor cells that differentiate into hair cells and supporting cells. In the Pou4f3-Cre:Rb1 flox/flox (Rb1 cKO) inner ear, utricular hair cells differentiate and survive into adulthood whereas differentiation and survival of cochlear hair cells are impaired. To comprehensively survey the pRb pathway in the mammalian inner ear, we performed microarray analysis of Rb1 cKO cochlea and utricle. P6 or 2-month control and Rb1 cKO littermates were euthanized and the inner ear tissues were dissected. Total RNA was extracted from the pooled samples. Technical duplicates of the pooled RNA were used for microarray.

2011-05-31 | E-GEOD-25732 | biostudies-arrayexpress

Expression data from Pou4f3-Rb1 cKO and control inner ear

2011-06-01 | GSE25732 | GEO

RNA-seq profiling of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish hair cell IP vs. whole fish IN

Project description:We have developed and tested the efficiency of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells (IP) compared to the whole fish transcriptome (IN). We show through RNA-seq that HA-tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts.

2018-04-24 | GSE102861 | GEO

RNA-seq expression profiling of hair-cells in zebrafish

Project description:Sensorineural hearing loss affects the majority of the elderly population. Mammalian hair cells (HC) do not regenerate and current stem cell and gene delivery protocols result only in immature hair cells like-cells. For this reason, characterization of the transcriptional cascades that lead to development and survival of inner ear HC is essential for designing molecular-based treatments for deafness. We employed a cell type-specific approach to analyze the transcriptomes of the mouse early postnatal auditory and vestibular sensory epithelia and of hair cells derived from zebrafish model.

2016-12-31 | GSE67479 | GEO

RNA-seq expression profiling of murine inner-ear hair cells

2016-06-20 | GSE67478 | GEO

Inner ear supporting cells are organized tissue-resident macrophages arranged like cobblestones.

Project description:Sensorineural hearing loss (SHL) is a relatively common disease, and studies have suggested viral infection as a major cause. In the inner ear, the blood-labyrinthine barrier prevents access of the peripheral immune system; therefore, the immune system remains poorly understood. Here we found that cochlear accessory supporting cells (SCs), which are anchored by tight junctions, are organized tissue-resident macrophages. Virus-infected supporting cells change into activated macrophages and protect audiosensory receptor hair cells (HCs) against virus infection by producing interferon (IFN)-α/β. Moreover, we also observed bacterial phagocytosis by SCs. However, tumour necrosis factor-related apoptosis-inducing ligand (Trail), produced by virus-infected SCs, induced sensory hair loss and HC death by necroptosis. Notably, corticosteroid, the only effective drug for SHL, inhibited the virus-induced macrophage change of SCs. These results revealed an inner ear immune system, and suggest a possible mechanism for virus-induced SHL.

2016-12-10 | GSE89556 | GEO

A Cell Type-Specific Approach to Elucidate the Role of miR-96 in Inner Ear Hair Cells

Project description:Mutations in miRNA-96, a microRNA expressed within the hair cells (HCs) of the inner ear, result in progressive hearing loss in both mouse models and humans. While previous studies have delved into miR-96 transcriptional cascades via whole organ of Corti microarray experiments of diminuendo (Mir96Dmdo) mice, they face limitations in pinpointing cell type-specific differentially expressed genes. This hinders the ability to conclusively determine if the effects of Mir96Dmdo are specifically within HCs and contribute to the observed abnormal Mir96Dmdo HC phenotype and determine the role of miR-96 in HCs. In this study, we generate the first HC-specific RNA-sequencing (RNA-seq) datasets from Mir96Dmdo; Atoh1/nGFP+ postnatal day 1 wildtype, heterozygous, and homozygous mutant mice. Our differential gene expression analysis between Mir96Dmdo homozygous mutant HCs compared to wildtype HCs identified 215 upregulated and 428 downregulated genes. Many significantly downregulated genes in Mir96Dmdo homozygous mutant HCs have established roles in HC development and/or known roles in deafness such as Myo15, Myo7a, Ush1c Gfi1, and Ptprq, some of which were not previously identified in other miR-96 datasets. In addition, active modules of protein-protein interaction networks of significantly downregulated genes in Mir96Dmdo homozygous mutant HCs reveal enrichment in GO terms with biological functions such as sound perception and endocytosis. Genes significantly upregulated in Mir96Dmdo homozygous mutant HCs, which are more likely to be direct targets of miR-96, show higher expression in wildtype supporting cells compared to wildtype HCs, suggesting a role of miR-96 in suppressing non-HC genes during HC development. Finally, all generated HC-specific Mir96Dmdo RNA-seq datasets from this manuscript are now publicly available in the miR-96 specific gEAR profile (https://umgear.org/p?l=miR96).

2024-05-09 | GSE255796 | 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