Laser-capture microdissection of maize kernel compartments for RNA-seq-based expression analysis

Shanshan Zhang, Dhiraj Thakare, Ramin Yadegari

Research output: ResearchChapter

Abstract

Laser-capture microdissection (LCM) enables isolation of single cells or groups of cells for a variety of downstream applications including transcriptome profiling. Recently, this methodology has found a more widespread use particularly with the advent of next-generation sequencing techniques that enable deep profiling of the limited amounts of RNA obtained from fixed or frozen sections. When used with fixed tissues, a major experimental challenge is to balance the tissue integrity needed for microscopic visualization of the cell types of interest with that of the RNA quality necessary for deep profiling. Complex biological structures such as seeds or kernels pose an especially difficult case in this context as in many instances the key internal structures such as the embryo and the endosperm are relatively inaccessible. Here, we present an optimized LCM protocol for maize kernel that has been developed specifically to enable profiling of the early stages of endosperm development using RNA-Seq.

LanguageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages153-163
Number of pages11
Volume1676
DOIs
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
Volume1676
ISSN (Print)1064-3745

Fingerprint

Laser Capture Microdissection
Zea mays
RNA
Endosperm
Cell Separation
Frozen Sections
Gene Expression Profiling
Seeds
Embryonic Structures

Keywords

  • Endosperm
  • Kernel
  • Laser-capture microdissection
  • Maize
  • Transcriptome

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Zhang, S., Thakare, D., & Yadegari, R. (2018). Laser-capture microdissection of maize kernel compartments for RNA-seq-based expression analysis. In Methods in Molecular Biology (Vol. 1676, pp. 153-163). (Methods in Molecular Biology; Vol. 1676). Humana Press Inc.. DOI: 10.1007/978-1-4939-7315-6_9

Laser-capture microdissection of maize kernel compartments for RNA-seq-based expression analysis. / Zhang, Shanshan; Thakare, Dhiraj; Yadegari, Ramin.

Methods in Molecular Biology. Vol. 1676 Humana Press Inc., 2018. p. 153-163 (Methods in Molecular Biology; Vol. 1676).

Research output: ResearchChapter

Zhang, S, Thakare, D & Yadegari, R 2018, Laser-capture microdissection of maize kernel compartments for RNA-seq-based expression analysis. in Methods in Molecular Biology. vol. 1676, Methods in Molecular Biology, vol. 1676, Humana Press Inc., pp. 153-163. DOI: 10.1007/978-1-4939-7315-6_9
Zhang S, Thakare D, Yadegari R. Laser-capture microdissection of maize kernel compartments for RNA-seq-based expression analysis. In Methods in Molecular Biology. Vol. 1676. Humana Press Inc.2018. p. 153-163. (Methods in Molecular Biology). Available from, DOI: 10.1007/978-1-4939-7315-6_9
Zhang, Shanshan ; Thakare, Dhiraj ; Yadegari, Ramin. / Laser-capture microdissection of maize kernel compartments for RNA-seq-based expression analysis. Methods in Molecular Biology. Vol. 1676 Humana Press Inc., 2018. pp. 153-163 (Methods in Molecular Biology).
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