Total RNA was extracted from the wild-type and bsu-q seedlings treated with flg22 or mock solution using the Spectrum Plant Total RNA kit (Sigma). cDNA libraries were constructed using a TruSeq RNA sample preparation kit (Illumina) according to the manufacturer’s instructions. Samples of three replicates were sequenced on an Illumina HiSEQ2000 sequencing machine. Mapping of reads to the reference genome (TAIR10) and calling differentially expressed genes was conducted via the iPlant collaborative Discovery Environment (de.iplantcollaborative.org/de/ )36 . Expression data was clustered and visualized with the TIGR MeV program (http://mev.tm4.org/ )37 (link). Scatter plots of flg22-responsive genes were analyzed with Microsoft Excel. GO analysis was performed with agriGO v2.0 (www.http://systemsbiology.cau.edu.cn/agriGOv2/index.php ) using default setting38 (link).
Protocol detail
Transcriptional Response to Flg22 Elicitation
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Variable analysis
independent variables
- Treatment (flg22 or mock solution)
- Gene expression (differentially expressed genes)
- Wild-type seedlings
- Bsu-q seedlings
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