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Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina

ABSTRACT: Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina

PROVIDER: PRJNA540843 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9004330_1.fastq.gz	Fastqsanger.gz
	SRR9004330_2.fastq.gz	Fastqsanger.gz
	SRR9004340_1.fastq.gz	Fastqsanger.gz
	SRR9004340_2.fastq.gz	Fastqsanger.gz
	SRR9004350_1.fastq.gz	Fastqsanger.gz

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Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina

Project description:Purpose: Single-cell RNA sequencing has revolutionized cell-type specific gene expression analysis. The goals of this study are to compare cell specific gene expression patterns between retinal cell types originating from the fovea and the periphery of human eyes. Methods: Independent libraries were prepared for foveal and peripheral samples of neural retina from three donors using the 10x Chromium system. Libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 will CellRanger(v3.0.1) and filters removed cells likely to be doublets or cells with a high proportion of mitochondrial reads. Clustering of cells with similar expression profiles was performed with Seurat (v2.3.4). Results: Independent libraries were prepared for foveal and peripheral samples of neural retina from three donors using the 10x Chromium system. Libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 will CellRanger(v3.0.1) and filters removed cells likely to be doublets or cells with a high proportion of mitochondrial reads. Clustering of cells with similar expression profiles was performed with Seurat (v2.3.4). Conclusions: Our study generates a large atlas of human retinal transcriptomes at the single cell level. We identified the majority of expected neural and supportive cell types, and describe regional differences in gene expression between the fovea and the periphery. Our results show that that single-cell RNA sequencing can be performed on human retina after cryopreservation, and that cone photoreceptors and Muller cells demonstrate region-specific patterns of gene expression.

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