Highly multiplexed spatial transcriptomics in bacteria

Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial messenger RNA. To overcome this challenge, we combined 1000-fold volumetric expansion with multiplexed error-robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissected the response of Escherichia coli to carbon starvation, systematically mapped subcellular RNA organization, and charted the…

• DC
  Dana-Farber/Harvard Cancer Center
• NI
  National Institutes of Health

  Award: P30DK034854
• AR
  Advanced Research Projects Agency
• HD
  Harvard Digestive Diseases Center, Harvard University

  Award: P30DK034854
• NC
  National Cancer Institute

  Awards: P30CA06516, P30DK034854