Transcript Identification Using Arrayed Hydrogels with TrapFISH.

3' single-cell transcriptomics aims to uncover transcript abundance across numerous cells to deepen our understanding of cellular diversity. However, sequencing capacity is often a bottleneck in these experiments, limiting the number of cells that can be profiled. In this study, we introduce trapFISH, a highly scalable proof-of-concept method that extends the capabilities of single-cell transcriptomics by embedding cells in hydrogel beads, arraying these beads in microfluidic chambers, and using probe-hybridization for targeted transcript quantification. This approach mitigates sequencing limitations by focusing on custom gene panels, enhancing throughput and facilitating the discovery of rare cell states. Moreover, microfluidic trapping removes the necessity for cell barcoding by linking transcriptional measurements directly with individual hydrogels. Our findings demonstrate that trapFISH improves scalability while maintaining high accuracy in identifying key cellular transcripts, opening new avenues in large-scale genomic profiling. By prioritizing biologically meaningful gene expression patterns, trapFISH provides a precise and efficient tool for single-cell characterization, expanding the flexibility and applicability of transcriptomics methods.