Pluto Bioinformatics

GSE149099: Transcriptomic comparison of young and aged choroid at the bulk and single-cell levels (bulk)

Bulk RNA sequencing

Purpose: The goals of this study were to identify cell specific expression patterns from infant and aged choroid, with a particular emphasis on how endothelial gene expression changes with age.; Methods: Independent libraries were prepared for infant and adult choroidal cells from seventeen human donors. Trephine punch biopsies were used to acquire central RPE and choroidal tissue (infants: 4 mm punch biopsy; adults: 8 mm hemisected punch biopsy). Poly-A selected RNA transcripts underwent 150 base-pair paired-end sequencing with an Illumina HiSeq 2000. 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 infant versus adult libraries. Differentially expressed genes (p-value < 0.00001, FDR < 0.001, cpm >2, logFC > 1) were input into WebGestalt for over-representation analysis. Aged choroidal samples were enriched in proinflammatory genes.; Conclusions: This study provides a transcriptomic comparison of infant and aged human donor choroid at the bulk and single-cell levels. The aged choroid, in particular the aged vasculature, is enriched in pro-inflammatory genes. SOURCE: Andrew Voigt University of Iowa