Laser Capture Microdissection-Based RNA-Seq of Barley Grain Tissues

Abstract

Spatiotemporal patterning throughout the plant body depends to a large degree on cell- and tissue-specific expression of genes. Subsequently, for a better understanding of cell and tissue differentiation processes during plant development it is important to conduct transcript analyses in individual cells or tissue types rather than in bulk tissues. Laser capture microdissection (LCM) provides a useful method for isolating specific cell types from complex tissue structures for downstream applications. Contrasting to mammalian cells, the texture of plant cells is more critical due to hard, cellulose-rich cell walls, large vacuoles, and air spaces which complicates tissue preparation and extraction of macromolecules, like DNA and RNA. In particular, developing barley seeds (i.e. grains) depict cell types with differences in osmomolarity (meristematic, differentiating and degenerating tissues) and contain high amounts of the main storage product starch. In this study, we report about methods allowing tissue-specific transcriptome profiling by RNA-seq of developing barley grain tissues from low-input RNA amounts. Details on tissue preparation, laser capture microdissection, RNA isolation, and linear mRNA amplification to produce high-quality samples for Illumina sequencing are provided. Particular emphasis was placed on the influence of the mRNA amplification step on the transcriptome data and the fidelity of deduced expression levels obtained by the developed methods. Analysis of RNA-seq data confirmed sample processing as a highly reliable and reproducible procedure that was also used for transcriptome analyses of different tissue types from barley plants.