Abstract

Significance Image-based approaches to single-cell transcriptomics offer the ability to quantify not only the copy number of RNAs within cells but also the intracellular RNA location and the spatial organization of cells within cultures or tissues. Here we report advances in multiplexed error-robust fluorescence in situ hybridization (MERFISH) that increase the measurement throughput by two orders of magnitude and allow gene expression profiling of ∼40,000 human cells in a single 18-h measurement. This drastic increase in throughput should facilitate the identification and study of rare populations of cells as well as the characterization of transcriptionally distinct cell types within large tissue regions.