  Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful
method for recovering gene expression data from an exponentially scalable
number of individual cells or nuclei. However, sci-RNA-seq is a complex
protocol that has historically exhibited variable performance on different
tissues, as well as lower sensitivity than alternative methods. Here we report
a simplified, optimized version of the three-level sci-RNA-seq protocol that is
faster, higher yield, more robust, and more sensitive, than the original
sci-RNA-seq3 protocol, with reagent costs on the order of 1 cent per cell or
less. We showcase the optimized protocol via whole organism analysis of an
E16.5 mouse embryo, profiling ~380,000 nuclei in a single experiment. Finally,
we introduce a "tiny sci-*" protocol for experiments where input is extremely
limited.
