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ABSTRACT: Single-cell RNA sequencing in MNU injured retina

PROVIDER: PRJNA1226294 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32419634.fastq.gz	Fastqsanger.gz
	SRR32419635.fastq.gz	Fastqsanger.gz
	SRR32419636.fastq.gz	Fastqsanger.gz
	SRR32419637.fastq.gz	Fastqsanger.gz
	SRR32419638.fastq.gz	Fastqsanger.gz

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Single-cell RNA sequencing of MNU injured mouse retina

Project description:We elucidate the role of prospero-related homeobox 1 (Prox1) in rendering the mammalian retina incompetent for MG(Muller glia cell)-derived regeneration. Prox1 accumulates in MG in the degenerating human and mouse retinas but not in those in the regenerating zebrafish retina. We investigated whether the transition of MG to proliferative MGPCs occurred in MNU-injured Prox1fg/fg;Chx10-CreERT2 mouse retinas through single-cell RNA sequencing analysis.

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The regeneration-responsive careg element monitors activation of Müller glia after MNU-induced damage in the zebrafish retina

Project description:We found that the zebrafish non-coding element careg, which is induced in regenerating fins and heart, also participates in retina regeneration. Its activation persisted mostly in Müller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration, we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells, we performed a single-cell RNA sequencing (scRNA-seq) experiment of retinas dissected from adult careg:EGFP zebrafish at 3, 7, and 10 dpMNU. Our control retinas were dissected from fish at 3 days after treatment with heat-inactivated MNU

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SMART-seq of MG lineages in MNU-injured retinas

Project description:We further investigated injury-induced gene expression changes selectively in MG cell lineages. The tdTom-labeled MG and their descendant cells were isolated via FACS from uninjured or MNU-injured Glast-CreERT;R26tdTom/+ mouse retinas, which were infected with either AAV2-Ctrl Ab or AAV2-alpha Prox1, and mRNA expression patterns of individual cells were analyzed using SMART (Switching Mechanism At the 5' end of RNA Template) sequencing methods. We could identify a lineage flow from resting MG to RPC-like cells via activated MG, along with pseudo-time progression.

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RNA-seq analysis of the DTA-injured retina

Project description:The goal of this study is to identify genes upregulated in the DTA-injured retina. Methods: Retinal mRNA profiles of control (DTAwt) and DTA (DTAmut) mice at day 1 and 5 post-injry were generated by deep-sequencing with Illumina sequencer. Results: RNA-seq tags were mapped to the mouse mm9 reference genome assembly using Tophat2 ver. 2.0.8b, with FPKM values caluculated with Cufflinks ver. 2.1.1 with the default option.Comparison of the genes upregulated in the DTA-injured retina at day 1 and 5 revealed commonly upregulated genes as well as the genes specific to day 1 and 5. Conclusions: Our study provides the detailed analysis of retinal transcriptomes in the DTA-injured retina.

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