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…

• HH
  Howard Hughes Medical Institute
• DR
  Damon Runyon Cancer Research Foundation
• HH
  Helen Hay Whitney Foundation
• AF
  Agency for Science, Technology and Research
• NI
  National Institutes of Health