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A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (RNA-Seq)

ABSTRACT: A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (RNA-Seq)

PROVIDER: PRJNA891334 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21935100_1.fastq.gz	Fastqsanger.gz
	SRR21935100_2.fastq.gz	Fastqsanger.gz
	SRR21935101_1.fastq.gz	Fastqsanger.gz
	SRR21935101_2.fastq.gz	Fastqsanger.gz
	SRR21935102_1.fastq.gz	Fastqsanger.gz

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A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (ATAC-Seq)

Project description:Lens epithelial explants consist of lens epithelial cells (P8 FVB/N mice) grown in vitro on their native basement membrane, the lens capsule. For decades, biologists have used lens epithelial explants to study lens fiber cell differentiation. However, the global change in the accessibility of the chromatin and transcriptome during the process of explanting and culture is unknown. Therefore, P8 FVB/N lens epithelial explants cultured in either unsupplemented media or media containing 50% bovine vitreous humor for one or five days were collected. Chromatin and RNA was collected for ATAC-sequencing and RNA-sequencing respectively. Differentially accessible regions and differentially expressed genes were identified for each condition to provide a genome wide view of chromatin architecture and gene expression during fiber cell differentiation in vitro. Vitreous humor generally increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had relatively little effect on the accessibility of most of the genes highly expressed in the lens epithelium despite dramatic reductions in the transcript levels of these genes.

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A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (RNA-Seq)

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A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants

Project description:A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants

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A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (ATAC-Seq)

Project description:A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (ATAC-Seq)

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A Transcriptomics Analysis of the Regulation of Fiber Cell Differentiation in the Absence of FGFRs and PTEN

Project description:The addition of 50% vitreous humor to the media bathing lens epithelial explants results in the induction of both lens fiber cell differentiation and a significant immune/inflammatory response. Although Fgfr loss blocks differentiation in lens epithelial explants, this loss can be partially rescued by deleting Pten, demonstrating an epistatic relationship between FGFR-signaling and PTEN. To investigate the functions of Fgfrs and Pten during lens fiber cell differentiation, we utilized a lens epithelial explant system and conducted RNA sequencing on vitreous humor-exposed explants lacking Fgfrs, or Pten or both Fgfrs and Pten. We found that Fgfr loss impairs both vitreous-induced differentiation and inflammation while the additional loss of Pten restores these responses. Additionally, vitreous exposure triggers a less pronounced immune response in explants lacking both Fgfrs and Pten than in wildtype explants, but a stronger immune response than in explants lacking only Fgfrs. Furthermore, transcriptomic analysis suggested that PDGFR-signaling in FGFR-deficient explants might be required to mediate the rescue of vitreous-induced fiber cell differentiation in explants lacking both Fgfrs and Pten. The blockage of β- crystallin induction in explants lacking both Fgfrs and Pten in the presence of a PDGFR-inhibitor supports this hypothesis. Our findings demonstrate that a wide array of genes associated with fiber cell differentiation are downstream of FGFR-signaling and that the vitreous-induced immune responses also depend on FGFR-signaling. Our data also demonstrates that many of the vitreous-induced gene expression changes Fgfr-deficient explants can be rescued in explants lacking both Fgfrs and Pten.

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Project description:Total RNA was isolated from three separate populations of human lens epithelial cells and three matching populations of lens cortical fiber cells. All samples were analyzed on separate microarrays. Keywords: repeat sample

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Project description:Genome-wide approach to identify the cell-autonomous role of Brg1 in lens fiber cell terminal differentiation. To examine roles of Brg1 in mouse lens development, a dnBrg1 transgenic construct was expressed using the lens-specific alphaA-crystallin promoter in postmitotic lens fiber cells. Morphological studies revealed abnormal lens fiber cell differentiation in transgenic lenses resulting in cataract. Electron microscopic studies showed abnormal lens suture formation and incomplete karyolysis (denucleation) of lens fiber cells. To identify genes regulated by Brg1, RNA expression profiling was performed in E15.5 embryonic wild type and dnBrg1 transgenic lenses. In addition, comparisons between differentially expressed genes in dnBrg1 transgenic, Pax6 heterozygous, and Hsf4 homozygous lenses identified multiple genes co-regulated by Brg1, Hsf4 and Pax6. Among them DNase IIbeta, a key enzyme required for lens fiber cell denucleation, was found downregulated in each of the Pax6, Brg1 and Hsf4 model systems. Lens-specific deletion of Brg1 using conditional gene targeting demonstrated that Brg1 was required for lens fiber cell differentiation and indirectly for retinal development but was not essential for lens lineage formation. Wild type and dnBrg1 transgenic lenses, 4 biological replicates each

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Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and their denucleation [lens tissue]

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A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants

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

2023-02-15 | GSE215953 | GEO