Sample multiplexing for retinal single-cell RNA-sequencing

Single cell RNA sequencing (ScRNA-seq) often requires sample pooling, but sample variance is rarely addressed. We perform scRNA-seq on retinal ganglion cells with retina-multiplexing to assess the whether this enables comparisons between retinas of an experiment. Retinal ganglion cells (RGCs) of Vglut2-Tdtomato-Ai9 mice were enriched and isolated by negative-rod immunopanning using an anti-CD73 antibody and Fluorescence-Activated Cell Sorting (FACS) selecting for positivity of a Thy1-APC antibody and Tdtomato expression. Cholesterol-modified-oligos were used during RGC isolation for multiplexing. Samples were prepared and sequenced with the use of the 10x Genomics 3' chromium platform.