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Mus musculus

ABSTRACT: RNA-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 in mice at P0

PROVIDER: PRJNA361513 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5179390.fastq.gz	Fastqsanger.gz
	SRR5179391.fastq.gz	Fastqsanger.gz
	SRR5179392.fastq.gz	Fastqsanger.gz
	SRR5179393.fastq.gz	Fastqsanger.gz
	SRR5179384.fastq.gz	Fastqsanger.gz

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Combined double knockout of Ezh2 and G9a leads to expression change in murine retinal ganglion cells

Project description:Purpose: The goal of this study is to evaluate H3K27me3 histone marks in retinal ganglion cells in Ezh2 (Math5Cre, Ezh2-/-) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-) knockout mutant mice at P1. Both Ezh2 and G9a are major epigenetic silencing machineries. Ezh2 mediates the trimethylation of lysine 27 on histone 3. Emerging evidences show an interdependence between Ezh2 and G9a to facilitate K27 trimethylation. Methods: P1 retinal ganglion cells were collected and chromatin immunoprecipitation was performed with EZ- CHIP kit from Millipore. Library preparation was done with Rubicon Genomics Thruplex DNAseq. Results: Here, we find a pool of common K27me3 target genes of Ezh2 and G9a in double knockout that leads to dysfunction in double mutant RGCs. Conclusion: This study provides the first Chip-seq analysis of K27me3 in murine RGCs. Our data supports that an interaction between Ezh2 and G9a is also evident in murine retinal ganglion cells. This work should be a framework for further study of retinal ganglion cells and retinal diseases.

2022-07-29 | GSE118011 | GEO

RNA-Seq and ChIP-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 and G9a in murine retinal ganglion cells at P0

Project description:Epigenetic mark deposition during embryonic development contribute to postnatal homeostasis and tissue stability. Previously, we found out that Ezh2 contributes critically to the function and postnatal cell survival in bipolar cells but not in retinal ganglion cells in the retina. (Yan et al. Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1. Sci Report. doi:10.1038/srep33887; (Cheng L, Wong LJ, Yan N, Han RC et al. Ezh2 does not mediate retinal ganglion cell homeostasis or their susceptibility to injury. PLoS One 2018;13(2):e0191853.). In this study, we used RNA-seq to define up- and down regulated genes in both Ezh2 and G9a deficient (Math5Cre; Ezh2f/fG9af/+; dKO) retinal ganglion cells (RGC) to evaluate the hypothesis of Ezh2 and G9a interaction that has been discussed in other tissues but in the retina. ChIP-Seq was applied to evaluate H3K27me3 histone marks in retinal ganglion cells in wild type (WT), Ezh2 (Math5Cre; Ezh2-/-, sKO) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-, dKO) knockout mutant mice at P1.

2022-07-26 | GSE136360 | GEO

RNA-Seq and ChIP-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 and G9a in murine retinal ganglion cells at P0

Project description:RNA-Seq and ChIP-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 and G9a in murine retinal ganglion cells at P0

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Molecular characterization of Notch1 positive progenitor cells in the developing retina

Project description:The oscillatory expression of Notch signaling in neural progenitors suggests that both repressors and activators of neural fate specification are expressed in the same progenitors. Since Notch1 regulates photoreceptor differentiation and contributes (together with Notch3) to ganglion cell fate specification, we hypothesized that genes encoding photoreceptor and ganglion cell fate activators would be highly expressed in Notch1 receptor-bearing (Notch1+) progenitors, directing these cells to differentiate into photoreceptors or into ganglion cells when Notch1 activity is diminished. To identify these genes, we used microarray analysis to study expression profiles of whole retinas and isolated from them Notch1+ cells at embryonic day 14 (E14) and postnatal day 0 (P0). To isolate Notch1+ cells, we utilized immunomagnetic cell separation. RNA from Notch1+ cells and whole retinas at E14 and P0 was extracted and used for microarray analysis. We processed individual samples that each contained 200,000-500,000 Notch1+ cells. A total of three independent biological replicates in the early stage (E14) of retinal development and four independent biological replicates in the late stage (P0) of retinal development were obtained for comparative profiling of Notch1+ cells and whole retinas.

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Bulk RNA-seq analysis of control and Dnmt3a conditional knockout (cKO) retinal ganglion cells at 2 days post optic nerve crush

Project description:Dnmt3a deficiency in retinal ganglion cells promotes axon regeneration in an optic nerve crush mouse model. To investigate the role of Dnmt3a in axon regeneration, retinal ganglion cells isolated from control and retinal ganglion cell-specific Dnmt3a knockout mice at 2 days post-crush were applied for Bulk RNA-seq analysis by NovaSeq platform.

2023-12-14 | GSE229033 | GEO

Whole genome bisulfite-seq analysis of control and Dnmt3a conditional knockout (cKO) retinal ganglion cells at 2 days post optic nerve crush

Project description:Dnmt3a deficiency in retinal ganglion cells promotes axon regeneration in an optic nerve crush mouse model. To investigate the contribution of Dnmt3a to DNA methylation and axon regeneration, retinal ganglion cells isolated from control and retinal ganglion cell-specific Dnmt3a knockout mice at 2 days post-crush were applied for whole genome bisulfite-seq analysis by Illumina NovaSeq 6000.

2023-12-14 | GSE229034 | GEO

TGFβ signaling in retinal tissue repair [Mus Musculus]

Project description:In mammals, retinal damage is followed by Müller glia cell activation and proliferation. While retinal gliosis persists in adult mammals after an insult or disease, some vertebrates, including zebrafish, have the capacity to regenerate. We believe we are the first group to show that gliosis is a fibrotic-like process in mammals’ eyes caused by differential activation of canonical and non-canonical TGFβ signaling pathways.

2019-11-03 | GSE132140 | GEO

Single nuclei RNA-seq analysis of control and Dnmt3a conditional knockout (cKO) of retinal ganglion cells at 2 days post optic nerve crush.

Project description:Dnmt3a deficiency in retinal ganglion cells promotes axon regeneration in an optic nerve crush mouse model. To investigate the role of Dnmt3a in axon regeneration, retinal ganglion cell nuclei were sorted from control and retinal ganglion cell-specific Dnmt3a knockout mice at 2 days post optic nerve crush and applied for single nuclei RNA-seq analysis by 10X Genomics technology.

2023-12-14 | GSE228627 | GEO

RNA-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 in mice at P0

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