RNA-seq of retinal microglia and non-microglial retina cells in WT (Bmal1f/f) and microglial Bmal1-KO (Bmal1-mg/-mg) mice

We discovered that Bmal1 knockdown in retinal microglia alters their diurnal clock gene expression, inflammatory gene expression, and morphology. Furthermore, we found that this disruption of diurnal physiology in microglia results in reduced scotopic visual function, retinal neurodegeneration, and abnormal wheel running behavior in mice, suggesting that maintenance of the microglial clock contributes to retinal homeostasis. Subsequently, we investigated transcriptional alterations in retinal microglia and non-microglial cells in the retina to uncover gene expression patterns that may explain these clock-dependent phenotypes and potentially identify homeostatic neuro-glial signaling mechanisms dependent on microglial clock biology. Overall design: We used tissue dissociation and fluorescent activated cell sorting methods to simulatenously isolate viable microglia (CD11b+, DAPI-) and non-microglia retina (CD11b-, DAPI-) cells from Bmal1f/f and Bmal1-mg/-mg mice and performed RNA-Sequencing on purified mRNA samples (n=4-5/condition).