Easy-Multiome enables joint profiling of gene expression and chromatin accessibility in single cells

Although methods for jointly profiling these modalities exist, plant applications remain limted because of complex workflows, inconsistent performance, and prohibitive costs. Here, we present easy-Multiome, a streamlined single-cell multiomic workflow that integrates a single in situ reverse transcription step into the standard droplet-based scATAC-seq protocol.

Using easy-Multiome, we profiled more than 20,000 nuclei from maize seedlings generating paired gene expression and chromatin accessibility data, with approximately 90% of nuclei containing both high-quality RNA chromatin accessibility profiles. The resulting transcriptome data resolved 16 clusters corresponding to nine major maize seedling cell types and enabled direct characterization of cell-type-specific chromatin accessibility from the same nuclei.