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Human photoreceptor cells from different macular subregions have distinct transcriptional profiles

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE169048 | GEO | 2021/05/13

REPOSITORIES: GEO

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Human photoreceptor cells from different macular subregions have distinct transcriptional profiles.

Project description:The human neural retina is a light sensitive tissue with remarkable spatial and cellular organization. Compared with the periphery, the central retina contains more densely packed cone photoreceptor cells with unique morphologies and synaptic wiring. Some regions of the central retina exhibit selective degeneration or preservation in response to retinal disease and the basis for this variation is unknown. In this study, we used both bulk and single-cell RNA sequencing to compare gene expression within concentric regions of the central retina. We identified unique gene expression patterns of foveal cone photoreceptor cells, including many foveal-enriched transcription factors. In addition, we found that the genes RORB1, PPFIA1 and KCNAB2 are differentially spliced in the foveal, parafoveal and macular regions. These results provide a highly detailed spatial characterization of the retinal transcriptome and highlight unique molecular features of different retinal regions.

| S-EPMC8330894 | biostudies-literature

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [bulk RNA-seq]

Project description:Purpose: The goals of this study were to identify cell specific expression patterns from the fovea, perifovea, and macular neural retina. Methods: Independent libraries were prepared for human foveal (1mm), perifoveal (4mm), and macular (8mm) regions of neural retina. Poly-A selected RNA transcripts underwent 150 base-pair paired-end sequencing with an Illumina HiSeq 4000. Reads were mapped to the human genome hg19 with STAR (version = 020201) and quantified with the featureCounts function from the Rsubread package (version = 1.28.1). Differential expression analysis was performed with edgeR (version = 3.26.8). Results: Differential expression analysis identified genes enriched in each retinal region. Conclusions: This study provides a transcriptomic comparison of foveal, perifoveal, and macular human neural retina at the bulk and single-cell levels.

2021-05-13 | GSE169046 | GEO

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [single-cell RNA-seq]

Project description:Purpose: The goals of this study were to identify expression patterns in foveal versus parafoveal cells isolated from the human retina. Methods: Independent libraries were prepared for foveal and parafoveal cells isolated from four human donors (donors 5-8). A foveal (1 mm) and parafoveal (4 mm) punch of neural retina was acquired from each donor. Each punch of neural retina was gently dissociated in papain (Worthington biochemical) for 1.25 hours before cryopreservation. Thawed cells were barcoded with the 10X chromium and resulting libraries were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build GRCh38 with CellRanger(v3.0.1) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Libraries from single-cell donors 5-8 were aggregated using canonical correlation analysis. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1). Results: A total of 34,493 cells were recovered after filtering with 139,962,070 corresponding reads. A total of 5,856 cells were recovered from foveal libraries while 28,637 cells were recovered from the parafoveal libraries. Clusters were assigned to known retinal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from the fovea versus the parafovea. Particular emphasis was given to regionally expressed genes in cone photoreceptor cells and Muller cells. Conclusions: This study provides a transcriptomic comparison of the foveal and parafoveal human retina at the bulk and single-cell levels. The foveal retina is transcriptomically distinct from the directly surrounding parafovea.

2021-05-13 | GSE169047 | GEO

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles

Project description:Human photoreceptor cells from different macular subregions have distinct transcriptional profiles

| PRJNA714961 | ENA

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [bulk RNA-seq]

Project description:Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [bulk RNA-seq]

| PRJNA714962 | ENA

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [single-cell RNA-seq]

Project description:Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [single-cell RNA-seq]

| PRJNA714963 | ENA

Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2

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

2019-09-23 | GSE116343 | GEO

Unique Transcriptional Profiles Underlie Osteosarcomagenesis Driven by Different p53 Mutants

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

2023-05-12 | GSE231852 | GEO

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

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

2014-10-04 | E-GEOD-62047 | biostudies-arrayexpress

microRNA expression profiles of distinct human and mouse mammary epithelial cell types

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

2016-02-20 | E-GEOD-67056 | biostudies-arrayexpress

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