Molecular codes for cell type specification in Brn3 retinal ganglion cells

Significance We report here transcriptome analysis by RNA sequencing (RNASeq) of genetically labeled and affinity-purified mouse retinal ganglion cell (RGC) populations. Using a previously established conditional knock-in reporter strategy, we label RGCs from which specific transcription factors have been removed and determine the consequences on transcriptional programs at different stages critical to RGC development. We find that Brn3b and Brn3a control only small subsets of Brn3–RGC–specific transcripts. We identify extensive combinatorial sets of RGC transcription factors and cell surface molecules and show that several RGC-specific genes can induce neurite-like processes cell autonomously in a heterologous system.