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      Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution

      1 , 2 , 1 , 1 , 1 , 2
      Science
      American Association for the Advancement of Science (AAAS)

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          Abstract

          Capturing the heterogeneous phenotypes of microbial populations at relevant spatiotemporal scales is highly challenging. Here, we present par-seqFISH (parallel sequential fluorescence in situ hybridization), a transcriptome-imaging approach that records gene expression and spatial context within microscale assemblies at a single-cell and molecule resolution. We applied this approach to the opportunistic pathogen Pseudomonas aeruginosa, analyzing about 600,000 individuals across dozens of conditions in planktonic and biofilm cultures. We identified numerous metabolic- and virulence-related transcriptional states that emerged dynamically during planktonic growth, as well as highly spatially resolved metabolic heterogeneity in sessile populations. Our data reveal that distinct physiological states can coexist within the same biofilm just several micrometers away, underscoring the importance of the microenvironment. Our results illustrate the complex dynamics of microbial populations and present a new way of studying them at high resolution.

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          Most cited references2

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          RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

          Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here, we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 to 1000 distinct RNA species in hundreds of individual cells. Correlation analysis of the ~10(4) to 10(6) pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.
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            In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus.

            Identifying the spatial organization of tissues at cellular resolution from single-cell gene expression profiles is essential to understanding biological systems. Using an in situ 3D multiplexed imaging method, seqFISH, we identify unique transcriptional states by quantifying and clustering up to 249 genes in 16,958 cells to examine whether the hippocampus is organized into transcriptionally distinct subregions. We identified distinct layers in the dentate gyrus corresponding to the granule cell layer and the subgranular zone and, contrary to previous reports, discovered that distinct subregions within the CA1 and CA3 are composed of unique combinations of cells in different transcriptional states. In addition, we found that the dorsal CA1 is relatively homogeneous at the single cell level, while ventral CA1 is highly heterogeneous. These structures and patterns are observed using different mice and different sets of genes. Together, these results demonstrate the power of seqFISH in transcriptional profiling of complex tissues.
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              Author and article information

              Contributors
              Journal
              Science
              Science
              American Association for the Advancement of Science (AAAS)
              0036-8075
              1095-9203
              August 12 2021
              August 13 2021
              August 12 2021
              August 13 2021
              : 373
              : 6556
              : eabi4882
              Affiliations
              [1 ]Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
              [2 ]Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
              Article
              10.1126/science.abi4882
              8454218
              34385369
              33bd6b0f-78bb-4e66-ae3e-4236c9533d04
              © 2021

              https://www.sciencemag.org/about/science-licenses-journal-article-reuse

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