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Identification of Long Noncoding RNAs in the Developing Endosperm of Maize

  • Eundeok Kim
  • Yuqing Xiong
  • Byung-Ho Kang
  • Sibum SungEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)

Abstract

Maize endosperm consists of three distinct types of tissues, including the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Compartmentalization of these tissues during endosperm differentiation makes the endosperm development an excellent model to study changes in gene expression during development. By utilizing cryo-dissection of developing endosperm, morphologically distinct samples can be obtained for transcriptome and epigenome analysis. Here, we describe methods for the isolation of tissues from developing maize endosperm and for the transcriptome analysis to identify novel long noncoding RNAs. The transcriptome data can be further analyzed to illustrate spatiotemporal changes in both coding and noncoding transcripts during the endosperm development.

Key words

Endosperm Long noncoding RNAs Transcriptome analysis Cryo-dissection Maize In situ hybridization 

Notes

Acknowledgments

B.H. Kang and S. Sung are supported by USDA NIFA Award AFRI grant (2011-67013-30119). B.H. Kang is also supported by the grants from the Research Grants Council (RGC) of Hong Kong (GRF14126116, C4011-14R, and AoE/M-05/12), Cooperative Research Program for Agriculture Science and Technology Development (Project No. 10953092018), and Rural Development Administration, Republic of Korea, and S. Sung is also supported by NIH (GM100108) and NSF (1656764).

Supplementary material

978-1-4939-9045-0_3_MOESM1_ESM.docx (40 kb)
Supplementary File 1. Python script used for filtering small RNAs X (DOCX 40 kb)
978-1-4939-9045-0_3_MOESM2_ESM.docx (21 kb)
Supplementary File 2. Python script used for filtering transcripts from transposable elements X (DOCX 20 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Eundeok Kim
    • 1
    • 2
  • Yuqing Xiong
    • 3
  • Byung-Ho Kang
    • 3
    • 4
  • Sibum Sung
    • 1
    • 5
    Email author
  1. 1.Department of Molecular Biosciences and Institute for Cellular and Molecular BiologyThe University of Texas at AustinAustinUSA
  2. 2.Department of BiologyUniversity of WashingtonSeattleUSA
  3. 3.Microbiology and Cell ScienceUniversity of FloridaGainesvilleUSA
  4. 4.School of Life Sciences, State Key Laboratory for AgrobiotechnologyThe Chinese University of Hong KongShatinChina
  5. 5.International Scholar, Kyung-Hee UniversitySuwonSouth Korea

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