Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell gene expression profile of adult cochlear explants over the course of hair cell regeneration stimulated by chemical reprogramming [CocktailVehicleAtoh1]

ABSTRACT: Single cell gene expression profile of adult cochlear explants over the course of hair cell regeneration stimulated by chemical reprogramming [CocktailVehicleAtoh1]

PROVIDER: PRJNA903159 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22334323_1.fastq.gz	Fastqsanger.gz
	SRR22334323_2.fastq.gz	Fastqsanger.gz
	SRR22334324_1.fastq.gz	Fastqsanger.gz
	SRR22334324_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Single cell gene expression profile of adult cochlear explants over the course of hair cell regeneration stimulated by chemical reprogramming [CocktailVehicleAtoh1]

Project description:Strategies to overcome irreversible cochlear hair cell (HC) damage and loss are of vital importance to develop a treatment for hearing loss. HC regeneration in adult cochlea relies on a two-phase process: 1) Reprogramming mature cochlear (SCs) to regain the properties of their younger selves; 2) Activating Atoh1, a gene responsible for HC fate-determining, in the reprogrammed adult SCs for HC regeneration. We have shown that, by transient co-activation of Myc and NICD (Notch1 intracellular domain), the adult mouse cochlea can be successfully reprogrammed to a relatively younger stage and regain progenitor capacity, with the regeneration of HCs following Atoh1 overexpression in vitro and in vivo. We identified a combination (the cocktail) of drug-like molecules composing of small molecules and siRNAs to activate the pathways of Myc, Notch1, Wnt and cAMP. To identify molecules to reprogram mature cochlear SCs and HC regeneration, we utilized single-cell RNA sequencing and uncovered the pathways and their target genes underlying chemical-mediated reprogramming. We used an in-house adult cochlea explant culture system and carried out single-cell RNA sequencing to examine the gene expression profiles of cochlear explants, in response to chemical-induced reprogramming. We compared gene expression profiles between Vehicle/ad.Atoh1 activation vs. Cocktail (chemical reprogramming)/ad.Atoh1 activation.

2023-06-01 | GSE218324 | GEO

Single cell gene expression profile of adult cochlear explants over the course of hair cell regeneration stimulated by Atoh1 activation [DoxVehicleAtoh1]

Project description:Strategies to overcome irreversible cochlear hair cell (HC) damage and loss are of vital importance to develop a treatment for hearing loss. HC regeneration in adult cochlea relies on a two-phase process: 1) Reprogramming mature cochlear (SCs) to regain the properties of their younger selves; 2) Activating Atoh1, a gene responsible for HC fate-determining, in the reprogrammed adult SCs for HC regeneration. We have shown that, by transient co-activation of Myc and NICD (Notch1 intracellular domain), the adult mouse cochlea can be successfully reprogrammed to a relatively younger stage and regain progenitor capacity, with the regeneration of HCs following Atoh1 overexpression in vitro and in vivo. To identify molecules to reprogram mature cochlear SCs and HC regeneration, we utilized single-cell RNA sequencing and uncovered the pathways and their target genes underlying MYC/NICD-mediated reprogramming. We used an in-house adult cochlea explant culture system and carried out single-cell RNA sequencing to examine the gene expression profiles of cochlear explants from a transgenic mouse model, rtTa/tet-Myc/-tet-NICD, in response to Dox-induced MYC/NICD co-activation. We compared gene expression profiles between Atoh1 activation vs. MYC/NICD/Atoh1 co-activation.

2023-06-01 | GSE218325 | GEO

RNA-seq analysis of neonatal mouse cochlear hair cells

Project description:This study examined transcripts that are enriched in neonatal mouse cochlear hair cells. Hair cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which the endogenous Atoh1 gene was fused with GFP Two replicates of GFP+ hair cells were compared with all other cochlear cell types that were GFP-

2015-03-01 | E-GEOD-65633 | biostudies-arrayexpress

Thyroid hormone augmentation accelerates hair cell maturation in human cochlear organoids

Project description:Outer and inner hair cells in the cochlea are essential for hearing, but are vulnerable to damage by genetic mutations and environmental insults, resulting in irreversible sensorineural hearing loss. Investigating these processes requires access to large numbers of human cochlear hair cells and the ability to precisely control genetic, biochemical, and environmental conditions. We recently established a new organoid system that recapitulates human cochlear differentiation. However, maturation of cochlear organoid cultures is inefficient, requiring several months to express the mature outer hair cell marker Prestin. To efficiently obtain fully functional outer hair cells, we tested the effects of the thyroid hormone thyroxine on hair cell maturation in human cochlear organoids. Thyroxine supplementation significantly increased the percentages of Prestin-positive hair cells in an age-dependent manner. Additionally, transcriptomic analyses revealed upregulation of mature outer hair cell genes and downregulation of immature hair cell genes in thyroxine-treated hair cells. Furthermore, some of the treated hair cells exhibited electromotility, a functional hallmark of mature outer hair cells. These results suggest that thyroid hormones accelerate the maturation of hair cells in human cochlear organoids, thereby useful for establishing an improved in vitro model for pre-clinical investigation on sensorineural hearing loss.

2025-12-17 | GSE292457 | GEO

RNA-seq analysis of neonatal mouse cochlear hair cells

2015-03-01 | GSE65633 | GEO

The cargos and roles of small extracellular vesicles from cochlear explants in cisplatin-induced ototoxicity

Project description:Small extracellular vesicles (sEVs) play an important role in intercellular communication as well as pathological development. Here, to explore the roles of sEVs in the progression of cisplatin-induced ototoxicity, we isolated sEVs from the conditioned culture medium of cisplatin-induced cochlear explants (Cis-sEVs) and the control group (Ctrl-sEVs) and profiled their cargos using label-free LC-MS/MS. Numerous proteins involved in the regulation of the damage response were enriched in the Cis-sEVs. Cltc, Cct2, and Hspa8, which are potentially involved in protein homeostasis and autophagy, are up-regulated in Cis-sEVs compared to Ctrl-sEVs but not in cisplatin-damaged cochlear tissue or in HEI-OC1 cell lysates.

2025-09-01 | PXD052123 | Pride

Identification of intermediate transcriptome states and synergistic effects of Isl1 in Atoh1-mediated cochlear hair cell conversion

Project description:Ectopic expression of Atoh1 in non-sensory supporting cells (SCs) in mouse cochleae induces their conversion to hair cells (HCs) in vivo. cHCs in multiple intermediate states of the conversion process that most closely resembled neonatal differentiating HCs, but differed from the progenitors. We further identified 52 transcription factors that are differentially expressed in cHCs, SCs, and mature HCs and confirmed that Isl1 synergistically enhanced the efficiency of Atoh1-mediated HC conversion in cochlear explants. Our results demonstrate that direct HC conversion from SCs in vivo follows a different path from normal development and requires multiple factors for maximum efficiency and completion.

2018-07-23 | GSE85983 | GEO

Gene expression during synaptic regeneration between cochlear hair cells and neurons

Project description:Significant changes in the expression of synaptic and inflammatory genes were observed early after damage, during regeneration of the fibers and synapses, and after completion of in vitro regeneration between afferent neurons and cochlear hair cells.

2020-09-14 | GSE130495 | GEO

The Study of Chinese Medicine Intervention on Apoptosis of Cochlear hair cells in C57BL/6J Aged Cochlea

Project description:Through the intervention of traditional Chinese medicine prescription on cochlear hair cell apoptosis of c57 mice to 7-month-old mice, the proteomic analysis of cochlear hair cell apoptosis of 7-month-old mice and 2-month-old mice in the non traditional Chinese medicine group was compared to try to find the target or related pathway of Chinese medicine affecting cochlear senile apoptosis.

2023-05-04 | PXD041998 |

Unraveling the Molecular Landscape of Lead-Induced Cochlear Synaptopathy: A Quantitative Proteomic Analysis

Project description:This study investigates how lead exposure triggers cochlear synaptopathy and hearing loss in mice. Young-adult CBA/J mice were given lead acetate in drinking water for 28 days. We assessed hearing thresholds, outer hair cell activity, and synaptic changes in the cochlea. Lead exposure raises hearing thresholds, indicating cochlear synaptopathy. Notably affects synapses in the basal turn without impacting outer hair cells. In addition to this, lead altered the abundance of 352 synaptic proteins, with the synaptic vesicle cycle pathway prominently affected. Lead-induced cochlear synaptopathy targets basal cochlear regions, implicating synaptic vesicle cycle signaling in hearing loss. Revealing specific mechanisms behind lead-induced hearing deficits enhances targeted interventions and preventive strategies, advancing our understanding of lead induced hearing loss.

2024-10-17 | PXD050415 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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