Methods that measure the transcriptomic state of thousands of individual cells have transformed our understanding of cellular heterogeneity in eukaryotic cells since their introduction in the past decade. While simple and accessible protocols and

Across biological systems, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. While low-dimensional dynamics can be extracted using RNA velocity, these algorithms

The rapid adoption of single-cell technologies has created an opportunity to build single-cell ‘atlases’ integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future

B cell and T cell receptor repertoires compose the adaptive immune receptor repertoire (AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that drives adaptive immune responses, which in turn is imprinted in each

In this chapter we describe contemporary methods employed to characterize the detailed features of individual neocortical pyramidal neurons in the mammalian brain. First, a brief overview is provided of widely used approaches to study the intrinsic