High-throughput in situ hybridization: Systematical production of gene expression data and beyond

Lars Geffers*, Gregor Eichele

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

1 Citation (Scopus)


A plethora of modern-day techniques allows the detailed characterization of the transcriptome on a quantitative level. Analyses, based on techniques such as cDNA microarrays or RNA-seq (whole transcriptome shotgun sequencing), are usually genome wide in scope and readily detect small changes in gene expression levels across different biological samples. However, when it comes to spatial localization of gene expression within the context of complex tissues, traditional methods of in situ hybridization remain unparalleled with regard to their cellular resolution. Here we review methods that extend classical in situ hybridization protocols and techniques to the special needs of high-throughput (HT) studies and which can be readily scaled up to a genomic level to cover organs or even whole organisms in great detail. Moreover, we discuss suitable HT instrumentation and address postproduction issues typically arising with HT pipelines such as annotation of expression data and database organization.

Original languageEnglish
Title of host publicationIn Situ Hybridization Methods
PublisherSpringer New York
Number of pages25
ISBN (Electronic)9781493923038
ISBN (Print)9781493923021
Publication statusPublished - 18 Feb 2015
Externally publishedYes


  • Annotation
  • Functional genomics
  • Gene expression analysis
  • In situ hybridization
  • Web databases


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