The Allen Institute for Immunology as a whole seeks to advance the fundamental understanding of the immune system by employing a full spectrum of -omics tools to understand the molecular pathways and mechanisms responsible for the development and progression through immune-driven pathology. Projects like the Human Immune Health Atlas, a comprehensive single-cell reference dataset that offers unprecedented insight into the landscape of healthy human immune cells from childhood through adulthood, are an example of the multi-team, high parameter, “big” science that the Allen Institute is known for. The challenge begins when it is time to develop smaller, targeted, panels to follow up on patterns and novel hypotheses revealed following data analysis. Here we will discuss the two phases of data generation at the Allen Institute for Immunology. Phase 1 being the development of high dimensional, highly robust protocols for immune cell interrogation by flow cytometry and single cell genomics and phase 2 being lower dimension image cytometry, high-throughput and automation compatible assays to investigate subsets of cohorts.

 

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