Transposon sequencing was performed as described previously42 (link). Briefly, a pooled transposon library was grown in the presence or absence of 1 μg/ml tunicamycin at 30 °C for 5 h. Genomic DNA was then harvested and prepared for Illumina high-throughput sequencing for identification of the genomic location of the transposon in the surviving mutant. Sequencing data was processed using the Tufts University Genomics Core Facility Galaxy server43 (link)–45 (link) and mapped to the genome of NCTC832 using Bowtie software46 (link). Mapped reads were processed to identify depleted genes using the Mann-Whitney U test. Genes that had a >5-fold change in the number of reads between control and treated samples were considered enriched or depleted, and the significance threshold was set to P < 0.05 after correcting for false discovery rate.
All genes that were considered a hit in any comparison were then compiled. The depletion ratio for each gene in each sample was then combined by geometric averaging (taking the sixth root of the product of all six depletion ratios). P values were combined by using the Chi Squared statistic with six degrees of freedom.
All genes that were considered a hit in any comparison were then compiled. The depletion ratio for each gene in each sample was then combined by geometric averaging (taking the sixth root of the product of all six depletion ratios). P values were combined by using the Chi Squared statistic with six degrees of freedom.
