Calcified Artery Preparation and Processing with Preserved Morphology and RNA for Digital Spatial Profiling

Hong Niu; Keisuke Kamada; Emily Beirne; Gale L. Tang

doi:10.3791/69159

Calcified Artery Preparation and Processing with Preserved Morphology and RNA for Digital Spatial...

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JoVE Journal Medicine

Calcified Artery Preparation and Processing with Preserved Morphology and RNA for Digital Spatial Profiling

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09:12 min

January 23, 2026

DOI: 10.3791/69159-v

Hong Niu*¹, Keisuke Kamada*¹, Emily Beirne², Gale L. Tang^1,3

¹Division of Vascular Surgery, Department of Surgery,University of Washington, ²Department of Laboratory Medicine and Pathology,University of Washington, ³Division of Vascular Surgery,VA Puget Sound Health Care System

This protocol includes a step-by-step workflow for calcified vascular specimens: tissue handling, decalcification, RNA validation, calcification level detection, and region-of-interest selection strategies on the Nanostring GeoMx Digital Spatial Profiler (DSP). The goal is to present a comprehensive method for preserving vascular tissue morphology and RNA for reliable spatial transcriptomic analysis.

Spatial transcriptomics offers an advantage over both single-cell RNA seq and bulk RNA seq by preserving spatial information within the tissue. By using tools like RNAscope, computational deconvolution, and publicly available single-cell datasets, it is possible to map cellular behavior to its niche and gene profiles and build an integrated view of tissue biology. This technology's exploding.

Two May 2025 Nature"papers focus on spatial transcriptomics studies. If we chart PubMed, the curve is even steeper:roughly 150 spatial papers in 2023, nearly 300 in 2024, and on pace to surpass 500 publications in 2025. Spatial transcriptomics has already reshaped several major research areas, like cancer biology, neuroscience, immunology, and developmental biology.

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