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RNA-seq analysis of neonatal mouse cochlear supporting cells

ABSTRACT: RNA-seq analysis of neonatal mouse cochlear supporting cells

PROVIDER: PRJNA325664 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3666050_1.fastq.gz	Fastqsanger.gz
	SRR3666050_2.fastq.gz	Fastqsanger.gz
	SRR3666060_1.fastq.gz	Fastqsanger.gz
	SRR3666060_2.fastq.gz	Fastqsanger.gz
	SRR3666860_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]

Project description:This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.

2016-07-01 | E-GEOD-83356 | biostudies-arrayexpress

RNA-seq analysis of neonatal mouse cochlear supporting cells [Treated AK]

Project description:This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6 after inhibition of the Notch signaling pathway. Cochleas from postnatal day 0 and postnatal day 5 were cultured for 24 hours in the gamma secretase inhibitor DAPT or DMSO as a vehicle control. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 0+24 hours culture and postnatal day 5 + 24 hours culture. (corresponding to P1 and P6). mRNA profiles of P0 and P5 supporting cells (GFP+) and all other cochlear cell types (GFP-) treated with DAPT or DMSO, two replicates each, were generated by deep sequencing using Illumna TruSeq.

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RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]

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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

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Characterizing adult cochlear supporting cell transcriptional diversity using single-cell RNA-Seq: Validation in the adult mouse and translational implications for the adult human cochlea

Project description:Characterizing adult cochlear supporting cell transcriptional diversity using scRNA-Seq Hearing loss is a significant disability that impacts 432 million people worldwide. A significant proportion of these individuals are dissatisfied with or do not have access to available treatment options which include hearing aids and cochlear implants. An alternative approach to restore hearing would be to regenerate lost cells, including hair cells in the adult cochlea. Such therapy would require restoration of the organ of Corti’s complex architecture, necessitating regeneration of both mature hair cells and supporting cells. We characterize the first single-cell adult cochlear supporting cell transcriptomes with the goals of: (1) demonstrating their transcriptional distinctiveness from perinatal cochlear supporting cells, (2) providing a metric for future attempts at regenerating mature cochlear supporting cells by identifying both cell type-specific and regional-specific expression, and (3) identify cell cycle gene expression present in adult supporting cells at the single cell level which may establish a basis for targeting cell cycle regulation pathways to force these cells out of quiescence.

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Single cell RNA sequencing analysis of mouse cochlear supporting cell transcriptomes with activated ERBB2 receptor, a candidate mediator of hearing restoration mechanisms

Project description:One potential approach to restore hearing is to enforce regeneration of hair cells (HCs) through induction of cellular signaling pathways in supporting cells (SCs) that promote dedifferentiation and proliferation. We previously showed that the constitutive activation of ERBB2 signaling in cochlear SCs indirectly promoted SC differentiation to HCs, both in vivo and in vitro. In the current study, we aimed at identifying mechanisms and molecular pathways activated in SCs with constitutive ERBB2 signaling. To this end, we used single cell RNA sequencing (scRNA-seq) to characterize the transcriptomes of individual neonatal mouse cochlear SCs that were induced to express ERBB2. We found that induction of ERBB2 in vivo resulted in generation of a new distinct cluster of cells with unique transcriptome. This population has de novo expression of two members of the small integrin-binding ligand n-linked glycoproteins (SIBLING) family and their regulators. We confirm expression of the SIBLING Secreted phosphoprotein 1 (SPP1) as one of the most up-regulated genes in response to ERBB2 activation. SPP1 mediates signaling through the CD44 receptor, promoting survival, proliferation, and differentiation of osteoblast lineage cells. Histological analyses of cochlear samples collected from young adult mice confirmed that induction of ERBB2 after noise exposure resulted in up-regulation of both SPP1 and its receptor CD44, and the formation of mitotic sensory stem-like cell aggregates in the organ of Corti. Our results suggest that ectopic activation of ERBB2-signaling in young adult mice secondarily promotes SPP1/CD44 signaling, possibly altering the microenvironment of the organ of Corti.

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RNA-seq analysis of neonatal mouse cochlear supporting cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-07-01 | E-GEOD-83357 | biostudies-arrayexpress

RNA-seq analysis of neonatal mouse cochlear supporting cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-07-01 | GSE83357 | GEO