Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting

Daniel Slane; Martin Bayer

doi:10.1007/978-1-4939-7125-1_3

Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting

Methods Mol Biol. 2017;1629:27-35. doi: 10.1007/978-1-4939-7125-1_3.

Authors

Daniel Slane¹, Martin Bayer²

Affiliations

¹ Department of Cell Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tuebingen, Germany.
² Department of Cell Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tuebingen, Germany. martin.bayer@tuebingen.mpg.de.

PMID: 28623577
DOI: 10.1007/978-1-4939-7125-1_3

Abstract

Fluorescence-activated cell sorting (FACS) is a powerful method for the analysis of cell type-specific transcriptome profiles, DNA or histone modifications, and chemical compounds. In plants, it has been employed mainly with root and shoot tissue in combination with cell wall digestion on cellular and nuclear content. However, many tissues are recalcitrant to cell separation and are therefore not readily accessible for FACS analysis. Here, we lay out a detailed protocol for the generation of transcriptional profiles from fluorescently labeled nuclei. The protocol described in this chapter has been used successfully to generate a transcriptional map of the early Arabidopsis thaliana embryo.

Keywords: Cell type; FACS; FANS; Microarray; Nuclear transcriptome; RNA amplification; mRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Arabidopsis / genetics
Flow Cytometry*
Gene Expression Profiling* / methods
Gene Expression Regulation*
Oligonucleotide Array Sequence Analysis / methods
Organ Specificity / genetics
Plants, Genetically Modified
Transcriptome*
Workflow