AACR 2024 Poster Presentation

George Emanuel, Yijia Sun, Bin Wang, Hao Wang, Renchao Chen, Timothy Wiggin, Yuan Cai, Jiang He
AGBT 2024

Improved spatially resolved single cell transcriptomic imaging in archival tissues with MERSCOPE®


The advent of tools enabling researchers to easily perform spatial transcriptomics with single cell resolution has enabled a revolution in the understanding of complex tissues. However, samples with degraded RNA or extensive protein crosslinking remain challenging for transcriptomic measurements. Formalin-fixed paraffin-embedded (FFPE) tissues are the most widely used sample types in clinical and molecular diagnosis, yet often are not collected under optimal protocols to preserve RNA. To accurately map gene expression in FFPE samples in situ and map subtle variations in the cellular composition, a spatial transcriptomics technique with high detection efficiency is required. The Vizgen® MERSCOPE® Platform enables Multiplexed Error Robust in situ Hybridization (MERFISH) technology and directly profiles the transcriptome of intact tissues with high sensitivity in high-quality samples. Here we present an enhanced MERFISH chemistry and workflow to perform MERFISH across a broad range of sample qualities. The updated workflow involves streamlined sample preparation and chemistry optimization to improve sensitivity for both high- and low-quality samples. We demonstrated its application in more than 5 sample types from mouse and human, including archival FFPE samples.