SH transcriptome-supplementary files .xlsx

After the quality control of the original transcriptomic data, we used Bowtie2 to compare clean reads to the reference gene sequence , and then RSEM was used to calculate the expression levels of genes and transcripts. The results in the table S1 showed that most genes in <i>P. aeruginosa</i> were expressed under both conditions. In order to reflect the correlation of gene expression between samples, Pearson correlation coefficients of all gene expression amounts between every samples were calculated, and then expression amount distribution analysis were performed. The obtained results are shown in Fig. S1A below. According to the gene expression level of each sample, a total of 2047 differentially expressed genes were detected by the threshold of fold changes&gt;2, Q value&lt;0.001, of which 368 genes were up-regulated and 1679 genes were down-regulated. The quantity of down regulated genes are significantly larger than the up-regulated genes. The results are shown in volcanic map of Fig. S1B.

在对原始转录组数据完成质量控制后，我们使用Bowtie2将clean reads（清洁读段）比对至参考基因序列，随后通过RSEM软件计算基因与转录本的表达水平。表S1的结果显示，铜绿假单胞菌（P. aeruginosa）在两种实验条件下均有多数基因得以表达。为反映样本间的基因表达相关性，我们计算了所有样本间全部基因表达量的皮尔逊相关系数，并开展了表达量分布分析，所得结果如图S1A所示。基于各样本的基因表达水平，我们以折叠变化（fold change）>2、Q值<0.001作为筛选阈值，共检测到2047个差异表达基因，其中上调基因368个，下调基因1679个。下调基因的数量显著多于上调基因，相关结果如图S1B的火山图所示。