Programmable transcript-specific enrichment for single-cell sequencing enables profiling of rare cell states

The widespread application of single-cell genomics technologies has accelerated our understanding of the breadth and depth of heterogeneity of cell states across diverse contexts. As single-cell RNA sequencing (scRNA-seq) has been the most popular modality used for profiling, many populations have been described primarily based on specific marker transcript profiles compared to classical cytometry approaches relying on protein expression. Additionally, many single cell studies require the isolation of nuclei from tissue, eliminating the ability to enrich learned rare cell states based on extranuclear protein markers. To address this limitation, we describe Programmable Enrichment via RNA Flow-FISH by sequencing (PERFF-seq), a scalable assay that enables single cell and single nuclei RNA-seq profiling from subpopulations of complex cellular mixtures solely defined by the abundance of RNA transcripts. Across vignettes of immune cell populations as well as nuclei from fresh frozen and formalin-fixed paraffin-embedded brain tissue, we demonstrate the enrichment of cell populations via RNA-based cytometry upstream of high-throughput scRNA-seq. Together, our approach provides a rational, programmable method for studying cell identities and transcriptional heterogeneity of rare populations identifiable by as few as one marker transcript, advancing the rational study of cellular diversity across fresh and archived tissue materials.