Differential expression genes in Arabidopsis under flg22 treatment

Seven-day-old Arabidopsis seedlings were treated with 4- μ M flg22 or water for 30 min. Total RNA was isolated from the seedlings using TRIzol reagent (Invitrogen). Library construction and sequencing were performed by Novogene (Tianjing, China). In-house Perl scripts were used to process the raw reads, and the clean data were obtained by calculating Q20, Q30, and GC content. The clean reads were aligned to the reference Arabidopsis genome using TopHat v2.0.12. The number of fragments per kilobase of transcript sequence per million base pairs sequenced was counted using HTSeq v0.6.1 (Trapnell et al., 2009). Differential expression analysis of seedlings treated with flg22 or water for two biological replicates (independent seedling samples grown and treated with flg22 or water under the same conditions) was performed using the DESeq R package (1.18.0). A model based on the negative binomial distribution was used to calculate P-values for differential expression, which were further adjuste