Automated pipeline for atlas-based annotation of gene expression patterns: Application to postnatal day 7 mouse brain

James Carson, Tao Ju, Musodiq Bello, Christina Thaller, Joe Warren, Ioannis A. Kakadiaris, Wah Chiu, Gregor Eichele

Research output: Contribution to journalArticlepeer-review

18 Scopus citations

Abstract

Massive amounts of image data have been collected and continue to be generated for representing cellular gene expression throughout the mouse brain. Critical to exploiting this key effort of the post-genomic era is the ability to place these data into a common spatial reference that enables rapid interactive queries, analysis, data sharing, and visualization. In this paper, we present a set of automated protocols for generating and annotating gene expression patterns suitable for the establishment of a database. The steps include imaging tissue slices, detecting cellular gene expression levels, spatial registration with an atlas, and textual annotation. Using high-throughput in situ hybridization to generate serial sets of tissues displaying gene expression, this process was applied toward the establishment of a database representing over 200 genes in the postnatal day 7 mouse brain. These data using this protocol are now well-suited for interactive comparisons, analysis, queries, and visualization.

Original languageEnglish (US)
Pages (from-to)85-95
Number of pages11
JournalMethods
Volume50
Issue number2
DOIs
StatePublished - Feb 2010

Keywords

  • Brain atlas
  • Comparison
  • Database
  • ISH
  • In situ hybridization
  • Landmarks
  • Mice
  • Rodents
  • Subdivision

ASJC Scopus subject areas

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

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