A USD 2.1 million NIH R01 award positions the University of Washington at the center of an emerging effort to overcome a fundamental throughput bottleneck in spatial transcriptomics, reflecting sustained NIH investment in enabling technologies that could reshape how tissue biology is studied at scale.
Spectral barcoding as a route beyond current multiplexing limits
The grant, administered by the National Institute of General Medical Sciences (NIGMS) and running from May 2026 through April 2030, funds the development of a library of more than 1,000 spectrally barcoded fluorescent probes designed for single-round, high-resolution spatial transcriptomics in both thin and thick tissue samples. The work is led by Daniel T. Chiu and Joshua Vaughan in the university's Department of Chemistry.
The core technical challenge the award addresses is well established in the field. Existing imaging-based spatial transcriptomics platforms — including commercial systems built on cyclic smFISH approaches — require multiple sequential rounds of staining, imaging, and probe removal to achieve high gene counts. Sequencing-based alternatives offer broader coverage but sacrifice spatial resolution and add cost and complexity. Neither approach is currently compatible with thick tissue sections, which preserve three-dimensional architecture and are increasingly used in research settings.
The UW research funding targets this gap directly. By encoding spectral identity into fluorescent probes and pairing them with DNA oligonucleotide adapters, the team aims to create a modular 1,024-probe library in which any mRNA target can be labeled by swapping the adapter sequence rather than redesigning the barcode probe itself. The architecture is intended to decouple probe synthesis from target selection, which could lower the barrier to adoption across diverse research applications.
From probe library to tissue atlas
University of Washington research grants in the spatial biology space have increasingly emphasized translational utility alongside technology development, and this award follows that pattern. Aims 2 and 3 of the project apply the new probe set to constructing a spatial cell atlas of the kidney glomerulus in adult and aged mouse tissue, complementing existing work at the institution on protein and carbohydrate imaging of the same structure.