Cell type-specific transcriptomics in the plant embryo using an adapted INTACT protocol

Joakim Palovaara*, Dolf Weijers

*Corresponding author for this work

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

1 Citation (Scopus)


Cells differentiate from undifferentiated precursors in order to establish the tissues of vascular plants. The different cell types and stem cells are first specified in the early embryo. How cell type specification is instructed by transcriptional control on a genome-wide level is poorly understood. A major hurdle has been the technical challenge associated with obtaining cellular transcriptomes in this inaccessible tissue. Recently, we adapted a two-component genetic labeling system called INTACT to isolate nuclei and generate a microarray-based expression atlas of the cell types in the early Arabidopsis thaliana embryo. Here we present a step-by-step description of the adapted INTACT protocol, as well as the approach to generate transcriptomic profiles. This protocol has been adapted to account for using seeds with embryos of various developmental stages as a starting material, and the relatively few cell type-specific nuclei that can be isolated from embryos.

Original languageEnglish
Title of host publicationPlant Embryogenesis
Subtitle of host publicationMethods and Protocols
EditorsM. Bayer
Place of PublicationNew York
PublisherHumana Press
Number of pages10
ISBN (Electronic)9781071603420
ISBN (Print)9781071603413
Publication statusPublished - 24 Jan 2020

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Cell type-specific
  • Embryo
  • Isolation
  • Nucleus
  • Transcriptome


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