RNA-Seq of Sphingomonas-irrE 40
Total RNA was extracted in biological triplicates from strains S. sp. NX-3 and S. sp. NX-R after cultured at 30 C and pH 7.0, and 40 C and natural pH for 20 h using TaKaRa RNAiso Plus kit. The concentration and purity of total RNA was determined using NanoDrop, and the integrity of the RNA was identified using Agilent 2100 and simulated electrophoresis gel images. The qualified RNA samples were sent to the Beijing Genomics Institute (BGI) for library constructing and sequencing. After data filtering, reference genome comparison and gene expression analysis, significant differentially expressed genes were filtered for genes with log2 fold change >1 (upregulation) or log2 fold change <-1 (downregulation) with p-value and FDR both <0.05. Significant differentially expressed genes were further cluster analyzed and functional enrichment analyzed to determine its most important biochemical metabolic pathways and signal transduction pathways.