How the transcriptomes of various cell types in a specific brain area differ is unclear. Here, Siegert et al. created an atlas of cell type transcriptomes for the mouse retina and found that each cell type was associated with the expression of a specific set of genes, including a specific set of transcription factor genes. This atlas may be useful in various ways, including the mapping of disease-associated genes to specific retinal cell types, providing insight into disease pathophysiology.