An optimized protocol for retina single-cell RNA sequencing [scRNA-Seq]

In this work, we compared different protocols to prepare single-cell suspensions used for scRNAseq and suggest an optimized dissociation protocol for mouse retina, which preserves cell morphology to a higher level leading to an overall increase of gene number per cell. We compared scRNAseq libraries generated with our optimized protocol to publicly available scRNAseq data of mouse retina. We further demonstrate a pipeline to reduce noise in scRNAseq caused by multiplets and ambient RNA. Mouse retina were disected and dissociated using different protocols. Libraries were generated using 10x Genomics' "Chromium Single Cell Gene Expression" system. We compared cell suspensions, gene number per cell, level of ambient RNA and the overall gene detection rate within accross cell types and protocols.