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

Science. 2015 Apr 24;348(6233):aaa6090. doi: 10.1126/science.aaa6090. Epub 2015 Apr 9.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Fibroblasts
  • Gene Expression Profiling / methods*
  • High-Throughput Screening Assays
  • Humans
  • In Situ Hybridization, Fluorescence / methods*
  • Molecular Imaging / methods*
  • RNA Probes
  • RNA, Messenger / analysis*
  • Single-Cell Analysis / methods*
  • Transcriptome*


  • RNA Probes
  • RNA, Messenger

Associated data

  • GEO/GSE67685