New tools for discovering the role sRNA plays in cellular regulation

Douglas P. Shepherd, Nan Li, Elizabeth Hong-Geller, Brian Munsky, James H. Werner

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations


We have used single molecule fluorescence in situ hybridization (smFISH) to study cell-to-cell heterogeneity of messenger RNA (mRNA) copy numbers for human host cells subject to a variety of external stimuli. In order to study the effect of various stimuli and genetic modifications on mRNA copy number, we have constructed an automated highthroughput multiplexed imaging system and data analysis package capable of localizing large numbers of individual mRNA transcripts in three dimensions. These experimental distributions of mRNA are used to refine and down-select regulatory models. Here we present a case example of Interleukin 1 alpha mRNA production in response to immune system stimulation. We propose a methodology for extending these methods to study the effect of small RNA on genetic expression by combining multiplexed imaging and numerical modeling at the system-level.

Original languageEnglish (US)
Title of host publicationSingle Molecule Spectroscopy and Superresolution Imaging V
StatePublished - 2012
Externally publishedYes
EventSingle Molecule Spectroscopy and Superresolution Imaging V - San Francisco, CA, United States
Duration: Jan 21 2012Jan 22 2012

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


ConferenceSingle Molecule Spectroscopy and Superresolution Imaging V
Country/TerritoryUnited States
CitySan Francisco, CA


  • genetic expression
  • multiplex imaging
  • single molecule imaging
  • smFISH
  • small interfering RNA

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging


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