Beyond the transcriptome: completion of act one of the Immunological Genome Project

•High-quality transcriptomes have been obtained for ∼270 mouse leukocyte subsets.•Discoveries include new phenotyping markers, new subsets, and novel regulators.•Current transcriptome studies are underway to evaluate perturbed states.

The Immunological Genome Consortium has generated a public resource (www.immgen.org) that provides a compendium of gene expression profiles of ∼270 leukocyte subsets in the mouse. This effort established carefully standardized operating procedures that resulted in a transcriptional dataset of unprecedented comprehensiveness and quality. The findings have been detailed recently in a series of publications providing molecular insights into the development, heterogeneity, and/or function of these cellular lineages and distinct subpopulations. Here, we review the key findings of these studies, highlighting what has been gained and how the knowledge can be used to accelerate progress toward a comprehensive understanding of the immune system.