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Vickovic S, Lötstedt B, Klughammer J, Mages S, Segerstolpe Å, Rozenblatt-Rosen O, Regev A. SM-Omics is an automated platform for high-throughput spatial multi-omics. Nat Commun 2022; 13:795. [PMID: 35145087 PMCID: PMC8831571 DOI: 10.1038/s41467-022-28445-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate SM-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.
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Affiliation(s)
- S Vickovic
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,New York Genome Center, New York, NY, USA. .,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
| | - B Lötstedt
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J Klughammer
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - S Mages
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Å Segerstolpe
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - O Rozenblatt-Rosen
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - A Regev
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Genentech, 1 DNA Way, South San Francisco, CA, USA.
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