scRNA-seq experiments on human foreskin fibroblasts, foreskin fibroblasts induced directly to retina pigment epithelium, and induced pluripotent stem cell derived retina pigment epithelium.

Regenerative medicine relies on basic research to find safe and useful outcomes that are only practical when cost-effective. The human eyeball requires the retinal pigment epithelium (RPE) for support and maintenance that interfaces the neural retina and the choroid at large. Nearly 200 million people suffer from age-related macular degeneration (AMD), a blinding multifactor genetic disease among other retinal pathologies related to RPE degradation. Recently, autologous pluripotent stem cell-derived RPE cells were prohibitively expensive due to time, therefore we developed a new simplified cell reprogramming system. We stably induced RPE-like cells (iRPE) from human fibroblasts by conditional overexpression of broad plasticity and lineage-specific pioneering transcription factors and treated some with nicotinamide and chetomin (iRPENC). iRPE cells showed features of modern RPE benchmarks and significant in-vivo integration in transplanted chimeric hosts. Herein, we provide the single-cell RNA (scRNA) sequencing profiling of the foreskin fibroblasts, iRPE, iRPENC, and model iPSC.RPE cells. Overall design: Cell culture samples were prepared as approximately 3,000 single cells and then sampled for scRNA-seq 10x Genomics 5' (v1.0 Chemistry) VDJ kit library construction with standard protocol for 5' Gene Expressoin libraries that skips Steps 4&5. Libraries were sequenced with paired-end reads on Illumina HiSeq X at one library per lane and then mapped to a custom reference human genome (hg38) using Cell Ranger (Version 3.1). related study: https://doi.org/10.1101/2020.07.27.215103

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