Gene expression analysis using conventional and imaging methods

Ulhas S. Kadam, Amy C. Lossie, Burkhard Schulz, Joseph Irudayaraj

Research output: Chapter in Book/Report/Conference proceedingChapter


Understanding the intricacies of gene expression is important for unraveling the mechanisms of growth, development, and maintenance of normal cell metabolism. Recently developed techniques such as cDNA-microarray hybridization or high-throughput RNA sequencing provide overall snapshots of the entire transcriptome of a given sample and have greatly shaped the development of biomedical research since the late 1990s. With the availability of next-generation sequencing technologies, whole transcriptome analysis is quickly becoming affordable and common practice in biological research. Quantification of gene expression is critical to understand gene regulatory networks, interpret epigenetic gene regulation, identify noncoding regulatory RNAs, and pinpoint genes involved in disease states or disorders. However, understanding the variability of gene expression from cell-to-cell demands a set of complementary tools that can be used to characterize gene expression networks in single cells. In this chapter, we review the recent advances in probe design chemistry, developments in imaging, and the need for spatial and temporal single-molecule transcript quantification. Additionally, we discuss the applicability of novel nanoparticle-based approaches for imaging RNA dynamics and quantification in medicine and molecular biology.

Original languageEnglish (US)
Title of host publicationDNA and RNA Nanobiotechnologies in Medicine
Subtitle of host publicationDiagnosis and Treatment of Diseases
Number of pages22
ISBN (Electronic)9783642368530
ISBN (Print)9783642368523
StatePublished - Jan 1 2013
Externally publishedYes


  • FISH
  • Fluorescent proteins
  • GFP
  • Gene expression
  • Imaging
  • Microscopy
  • Molecular beacons
  • Nanoparticle
  • Quantification
  • RNA-seq
  • mRNA
  • qRT-PCR

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)


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