Whole-organism spatial transcriptomics at single-cell resolution in C. elegans

Spatial transcriptomics has advanced our understanding of tissue organization by mapping gene expression in its native context yet applying these techniques to whole organisms remains a significant challenge. Caenorhabditis elegans is well-suited to whole organism-level analysis because its compact size, transparency, reproducible anatomy, and genetic tractability make it possible to link molecular and cellular changes to circuit function and behavior within the same animal. However, current transcriptomic approaches in C. elegans are often limited by spatial resolution or multiplexing capacity, making it challenging to profile multiple gene expression patterns across intact worms while preserving spatial context. Here, we present a single-molecule fluorescence in situ hybridization workflow that enables multiplex imaging with single-cell resolution across the entire worm. This approach allows sequential imaging of one gene per fluorescent channel using two channels across 20 hybridization rounds, enabling the profiling of up to 40 genes while preserving spatial context. We further provide a curated marker-gene panel for reproducible neuron identification, which, together with probabilistic assignment of transcripts to segmented nuclei, enables quantitative measurements of gene expression levels. We used this method to identify up to 86 neuronal classes and reveal sex- and neuron-specific expression patterns at single-cell resolution. Together, these results establish a scalable framework for the spatial analysis of gene expression and cell identity in intact C. elegans.