title: RNA-Seq of Bacillus aryabhattai
design: Five-day-old Arabidopsis plants were treated with 30 mL (4.77  109 CFU/mL) of B. aryabhattai. The bacterium was well established 72 h post-inoculation. Leaves, stems, and roots from five plants were collected after establishment. Plants treated with water were used as a control. Treatments and controls were repeated three times per group. Total RNA was isolated using the Qiagen RNeasy Midi Kit (Hilden, Germany), and the concentration of total RNA was determined using spectrometry. After isolation of the total RNA, eukaryotic mRNA was enriched using oligo (dT) beads. The samples were sequenced using an Illumina HiSeq 2000 (Personalbio Co. (Shanghai, Peoples Republic of China). High-quality reads were processed using the Perl script, and the differentially expressed genes were identified using the edgeR package [54]. Genes with a fold change  2 were considered significantly differentially expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to characterize the differentially expressed genes [55, 56]. In addition, the GO annotations were analyzed using Blast2GO software [57, 58].