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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: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [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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Liu Y, Lu Y, Chen G, Wang Q. Recent Progress of Hybrid Optical Probes for Neural Membrane Potential Imaging. Biotechnol J 2020; 15:e2000086. [PMID: 32662937 DOI: 10.1002/biot.202000086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/04/2020] [Indexed: 12/17/2022]
Abstract
The neural membrane potential of nerve cells is the basis of neural activity production, which controls advanced brain activities such as memory, emotion, and learning. In the past decades, optical voltage indicator has emerged as a promising tool to decode neural activities with high-fidelity and excellent spatiotemporal resolution. In particular, the hybrid optical probes can combine the advantageous photophysical properties of different components such as voltage-sensitive molecules, highly fluorescent fluorophores, membrane-targeting tags, and optogenetic materials, thus showing numerous advantages in improving the photoluminescence intensity, voltage sensitivity, photostability, and cell specificity of probes. In this review, the current state-of-the-art hybrid probes are highlighted, that are designed by using fluorescent proteins, organic dyes, and fluorescent nanoprobes as the fluorophores, respectively. Then, the design strategies, voltage-sensing mechanisms and the in vitro and in vivo neural activity imaging applications of the hybrid probes are summarized. Finally, based on the current achievements of voltage imaging studies, the challenges and prospects for design and application of hybrid optical probes in the future are presented.
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Affiliation(s)
- Yongyang Liu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yaxin Lu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Guangcun Chen
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qiangbin Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.,College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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