High-resolution expression profiling of selected gene sets during plant immune activation

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Ding, Pingtao, Ngou, Bruno Pok Man, Furzer, Oliver J., Sakai, Toshiyuki, Shrestha, Ram Krishna, MacLean, Dan and Jones, Jonathan D. G. (2020) High-resolution expression profiling of selected gene sets during plant immune activation. Plant Biotechnology Journal, 18 (7). pp. 1610-1619. ISSN 1467-7644

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Abstract

The plant immune system involves detection of pathogens via both cell-surface and intracellular receptors. Both receptor classes can induce transcriptional reprogramming that elevates disease resistance. To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP-I). We designed and synthesized biotinylated single-strand RNA bait libraries targeted to a subset of defense genes, and generated sequence capture data from 99 RNA-seq libraries. We built a data processing pipeline to quantify the RNA-CAP-I-seq data, and visualize differential gene expression. Sequence capture in combination with quantitative RNA-seq enabled cost-effective assessment of the expression profile of a specified subset of genes. Quantitative sequence capture is not limited to RNA-seq or any specific organism and can potentially be incorporated into automated platforms for high-throughput sequencing.

Item Type: Article
Additional Information: © 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Uncontrolled Keywords: arabidopsis,biosynthesis,defense responses,disease resistance,essential component,isochorismate,nlr,read alignment,repression,salicylic-acid,systemic acquired-resistance,data visualization,high-resolution expression profiling,plant immunity,quantitative rna-seq,sequence capture,transcriptional regulation
Faculty \ School: Faculty of Science > The Sainsbury Laboratory
Faculty of Science > School of Biological Sciences
UEA Research Groups: Faculty of Science > Research Groups > Plant Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 01 Feb 2020 04:25
Last Modified: 22 Oct 2022 05:48
URI: https://ueaeprints.uea.ac.uk/id/eprint/73946
DOI: 10.1111/pbi.13327

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