High-plex Multiomic Analysis in FFPE at Subcellular Level by Spatial Molecular Imaging
Emily A. Brown,
Derek L Buhr,
Ryan G Garrison,
Mark T. Gregory,
Margaret L. Hoang,
Emily E. Killingbeck,
Tae Kyung Kim,
Zachary R. Lewis,
Jeffrey S Nelson,
Giang T Ong,
Evan P Perillo,
Joseph C Phan,
Aster W Wardhani,
Corey A Williams-Wietzikoski,
Joseph M. Beechem
Posted 04 Nov 2021
bioRxiv DOI: 10.1101/2021.11.03.467020
Posted 04 Nov 2021
The Spatial Molecular Imaging platform (CosMx SMI, NanoString, Seattle, WA) utilizes a high-plex in-situ imaging chemistry for both RNA and protein detection. This automated instrument provides 1000's of plex, at high sensitivity (1 to 2 copies/cell), very low error rate (0.0093 false calls/cell), and background (~0.04 counts/cell). The imaging system generates three-dimensional super-resolution localization of analytes (< 50 nm in the X-Y plane), at ~ 1 million cells per sample, four samples per run. Cell segmentation is antibody-based, compatible with FFPE samples. Multiomic data (980 RNAs, 108 proteins) were measured at subcellular resolution using FFPE tissues (non-small cell lung (NSCLC) and breast cancer) and allowed identification of over 18 distinct cell types, 10 unique tumor microenvironments, and 100 pairwise ligand-receptor interactions. Over 800,000 single cells and ~260 million transcripts data are released into the public domain allowing extended data analysis by the entire spatial biology research community.
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