Drop-seq is a technology we developed for highly parallel analysis of RNA expression in thousands of individual cells. Drop-seq works by encapsulating individual cells into vast numbers of nanoliter-sized droplets, together with DNA-barcoded beads that uniquely identify the droplets. We described Drop-seq in a paper in 2015, and subsequent commercial technologies have been built on this approach. We have made Drop-seq open-source, and hundreds of labs have adopted it; detailed protocols and software are available on the Drop-seq web site.
The mammalian brain is composed of a large, unknown number of specialized cell types whose complex interactions drive behavior. Unbiased, large-scale gene expression profiling in individual cells offers an opportunity to systematically characterize cellular specialization within the nervous system. We used Drop-seq, which enables unbiased assessment of gene expression from thousands of individual cells, to generate profiles from 690,000 cells in nine tissues of the adult mouse brain: frontal cortex (156,000), posterior cortex (99,000), striatum (77,000), cerebellum (26,000), hippocampus (113,000), substantia nigra/ventral tegmental area (44,000), globus pallidus externus/nucleus basalis (66,000), thalamus (89,000), and entopeduncular nucleus (19,000). To identify distinct patterns of co-expression, we performed independent component analysis (ICA) on each of the nine individual tissue datasets. ICA identified both biologically derived signals—including those corresponding to canonical cell type distinctions and those with spatially graded patterns—as well as to technical signals—including those that were highly replicate-dependent, defined cell "doublets", or were correlated with tissue processing. We retained 601 non-technical ICs for use in graph-based clustering, partitioning cells into 565 distinct groups. These populations encompassed all known major cell classes in the nervous system, including neurons, astrocytes, microglia, oligodendrocytes and polydendrocytes, endothelial cells, and cells of the choroid plexus. Our analysis uncovers numerous undescribed cell types and states across the nervous system.
Saunders, A.*, Macosko, E.*, Wysoker, A., Goldman, M., Krienen, F., Bien, E., Baum, M., Wang, S., Goeva, A., Nemesh, J., Kamitaki, N., Brumbaugh, S., Kulp, D. and McCarroll, S. A Single-Cell Atlas of Cell Types, States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse Brain. Submitted.