title: RNA-Seq of E.coli BW25113 CRISPRi
design: 400ng of total RNA from each sample was used for generating cDNA libraries following the RNAtag-Seq protocol. PCR amplified cDNA libraries were sequenced on an Illumina NextSeq500 generating a high sequencing depth of ~7.5 million reads per sample. Raw reads were demultiplexed by 5 and 3 indices, trimmed to 59 base pairs, and quality filtered (96% sequence quality>Q14). Filtered reads were mapped to the corresponding reference genome using bowtie2 with the-very-sensitive option (-D 20 R 3 N 0 L 20 i S, 1, 0.50). Mapped reads were aggregated by feature Count and differential expression was calculated with DESeq2. In each pair-wise differential expression comparison, significant differential expression is filtered based on two criteria: |log2foldchange| > 1 and adjusted p-value (padj) <0.05. All differential expression comparisons were made between WT and paaBmutant either in LB or under TMP/SMX treatment. The reproducibility of the transcriptomic data was confirmed by an overall high Spearman correlation across biological replicates (R > 0.95).