UC Berkeley

Multicellular organisms rely on diverse cell types to carry out the multitude of tasks necessary

for complex life. Understanding the interplay between cell populations within a tissue

or organism is a major goal of biological and medical research. In pursuit of this aim, recent

advances in micro

uidics and molecular biology have propelled single-cell RNA-sequencing

(scRNA-seq) to the forefront of cell population analysis. Routine scRNA-seq experiments

can prole tens of thousands of genes from tens of thousands of cells in parallel, oering a

platform ripe for technological development, a sandbox in which a clever molecular biologist

may develop more varied experiments at unprecedented scale and depth. Accordingly, we

have made signicant inroads toward the goals of simultaneous RNA/epitope quantication

and ultra-low-cost library preparation, and we have expanded the capacity of scRNA-seq

with a novel sample multiplexing method. We demonstrate the power of parallel cell population

analysis with a high-resolution screen of experimental perturbations, introducing a

new paradigm in which scRNA-seq is used to understand a cell population at multiple scales

with unprecedented depth of information.