Author:
He Shanshan,Bhatt Ruchir,Brown Carl,Brown Emily A.,Buhr Derek L.,Chantranuvatana Kan,Danaher Patrick,Dunaway Dwayne,Garrison Ryan G.,Geiss Gary,Gregory Mark T.,Hoang Margaret L.,Khafizov Rustem,Killingbeck Emily E.,Kim Dae,Kim Tae Kyung,Kim Youngmi,Klock Andrew,Korukonda Mithra,Kutchma Alecksandr,Lee Erica,Lewis Zachary R.,Liang Yan,Nelson Jeffrey S.,Ong Giang T.,Perillo Evan P.,Phan Joseph C.,Phan-Everson Tien,Piazza Erin,Rane Tushar,Reitz Zachary,Rhodes Michael,Rosenbloom Alyssa,Ross David,Sato Hiromi,Wardhani Aster W.,Williams-Wietzikoski Corey A.,Wu Lidan,Beechem Joseph M.
Abstract
AbstractThe Spatial Molecular Imaging platform (CosMxTM 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.
Publisher
Cold Spring Harbor Laboratory