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High‐resolution expression profiling of selected gene sets during plant immune activation
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 quantita...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292544/ https://www.ncbi.nlm.nih.gov/pubmed/31916350 http://dx.doi.org/10.1111/pbi.13327 |
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author | Ding, Pingtao Ngou, Bruno Pok Man Furzer, Oliver J. Sakai, Toshiyuki Shrestha, Ram Krishna MacLean, Dan Jones, Jonathan D. G. |
author_facet | Ding, Pingtao Ngou, Bruno Pok Man Furzer, Oliver J. Sakai, Toshiyuki Shrestha, Ram Krishna MacLean, Dan Jones, Jonathan D. G. |
author_sort | Ding, Pingtao |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7292544 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-72925442020-06-15 High‐resolution expression profiling of selected gene sets during plant immune activation Ding, Pingtao Ngou, Bruno Pok Man Furzer, Oliver J. Sakai, Toshiyuki Shrestha, Ram Krishna MacLean, Dan Jones, Jonathan D. G. Plant Biotechnol J Research Articles 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. John Wiley and Sons Inc. 2020-01-27 2020-07 /pmc/articles/PMC7292544/ /pubmed/31916350 http://dx.doi.org/10.1111/pbi.13327 Text en © 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Ding, Pingtao Ngou, Bruno Pok Man Furzer, Oliver J. Sakai, Toshiyuki Shrestha, Ram Krishna MacLean, Dan Jones, Jonathan D. G. High‐resolution expression profiling of selected gene sets during plant immune activation |
title | High‐resolution expression profiling of selected gene sets during plant immune activation |
title_full | High‐resolution expression profiling of selected gene sets during plant immune activation |
title_fullStr | High‐resolution expression profiling of selected gene sets during plant immune activation |
title_full_unstemmed | High‐resolution expression profiling of selected gene sets during plant immune activation |
title_short | High‐resolution expression profiling of selected gene sets during plant immune activation |
title_sort | high‐resolution expression profiling of selected gene sets during plant immune activation |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292544/ https://www.ncbi.nlm.nih.gov/pubmed/31916350 http://dx.doi.org/10.1111/pbi.13327 |
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