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AGBT 2022 Poster: In Situ Single-cell Transcriptomic Imaging in Formalin-fixed Paraffin-embedded Tissues with MERSCOPETM

Jiang He, Lizhi He, Timothy Wiggin, Alex S Genshaft, Rob Foreman, Natalia Petrenko, Nicholas Fernandez, Renchao Chen, Colles Price, George Emanuel

Formalin-fixed paraffin-embedded (FFPE) tissues are widely used clinical sample types for histology and molecular diagnosis. However, due to RNA degradation and protein cross-linking, FFPE samples are often challenging for single-cell transcriptomic analysis. Vizgen’s in situ spatial genomics platform MERSCOPETM, built on multiplexed error robust in situ hybridization (MERFISH) technology, directly profiles intact tissue’s transcriptome with subcellular spatial resolution.

Here, we present a workflow to perform in situ single-cell transcriptomic imaging in FFPE tissue sections and demonstrate MERFISH imaging in more than 10 FFPE tissue types from mouse and human donors, including archival clinical samples. For each tissue type, hundreds of thousands of cells were captured, generating hundreds of millions of counts for profiled genes. Notably, we found that our FFPE workflow performs maintains the high accuracy and detection efficiency of our fresh frozen (FF) protocol in matched samples. Furthermore, we demonstrate that the MERSCOPETM FFPE workflow is compatible with protein imaging through simultaneous cell boundary staining and Vizgen’s soon-to-be-released protein co-detection product, enabling true cell atlassing in complex tissue like cancer. Combining these technologies to fit your experimental design, the MERSCOPE Platform makes spatial genomics inquiries accessible with diverse sample preservation methods.

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