High-resolution Expression Profiling of Selected Gene Sets during Plant Immune Activation
High-resolution Expression Profiling of Selected Gene Sets during Plant Immune Activation
复制标题
植物免疫激活过程中选定基因集的高分辨率表达谱
DOI：
10.1101/775973
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Ding P
中科院分区：
文献类型：
--
作者：
Ding P
植物免疫系统涉及通过细胞表面和细胞内受体检测病原体。这两种受体类别都可以诱导转录重编程，从而提高抗病性。为了评估植物免疫过程中的差异基因表达，我们开发并部署了定量序列捕获（CAP-I）。我们设计并合成了靶向防御基因子集的生物素化单链RNA诱饵文库，并从99个RNA测序文库中生成了序列捕获数据。我们建立了一个数据处理管道来量化RNA-CAP-I-seq数据，并可视化差异基因表达。序列捕获与定量RNA-seq相结合，能够对特定基因子集的表达谱进行成本效益评估。定量序列捕获不限于RNA测序或任何特定的生物体，并且可以潜在地并入自动化平台以进行高通量测序。
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.