MERFISH profiling of mouse retinal ganglion cell layer on wholemount

We optimized a workflow combining imaging-based spatial transcriptomics (MERFISH) and immunostaining on ganglion cell layer retinal flatmounts of C57/Bl6J mice.The MERFISH data shows molecularly-defined retinal ganglion cell types types exhibited non-uniform distributions. We also analyzed local neighborhoods for each cell and registered several RGC types as enriched in the perivascular niche. We recovered the spatial distribution of cell types in the mouse ganglion cell layer (GCL) by using the Vizgen MERSCOPE platform, which measured the expression of 140 genes in each of those cells. Cells were identified via boundary staining provided by Vizgen, and RNA transcripts were assigned to them via cell segmentation. There are 6 biological replicates, 3 of which contain costaining for CD31. Separately, there are 2 biological replicates with costaining of Opn4. Each biological replicate consists of multiple separately imaged tissue regions due to the 12 micrometer imaging limit.