Comparative RNA-Seq data for L. interrogans sv. Manilae L495 wild-type and perRA strains cultivated in dialysis membrane chambers (DMCs).

The genome sequence of L. interrogans sv. Manilae strain UP-MMC-NIID LP (accession numbers NZ_CP011931.1, NZ_CP011932.1 and NZ_CP011933.1) was used for mapping and differential gene expression analysis. All non-coding RNAs and pseudogenes were removed before DESeq2 analysis. Column A: RefSeq locus tag. Column B: Locus tag. Column C: L. interrogans serovar Copenhageni strain Fiocruz L1-130 (accession numbers NC_005823.1 and NC_005824.1) orthologs identified using OrthoVenn 2.0 [202]. Dashes (-) indicate genes for which no clear ortholog was identified. Column D: Description of gene product, following genome annotation. Columns E, F: Clusters of Orthologous Group (COG) classifications based on MicroScope [187]. Column G: Fold-regulation of the corresponding gene based on RNA-Seq analysis by Zavala-Alvarado et al. [93, 94] performed using the same strains cultivated in vitro. Positive and negative numbers indicate upregulation and repression, respectively, in the WT compared to the mutant strain. Dashes (-) indicate genes that are not differentially regulated at least 3-fold (p≤0.05) by PerRA in vitro. Column H: Fold-regulation determined using DESeq2 based on WT vs. perRA mutant RNA-Seq analysis using leptospires cultivated within DMCs. Column I: Type of regulation by PerRA in DMCs. Genes expressed at ≥3-fold higher/lower levels in the WT vs. mutant with a False-discovery rate-adjusted-p value (q) ≥0.05 were considered differentially expressed. “NO” indicates genes that are not regulated by PerRA in DMCs; “Up” indicates genes upregulated by PerRA in DMCs (expressed at lower levels in the mutant vs. WT); “Down” indicates genes downregulated by PerRA in DMCs (expressed at higher levels in the mutant vs WT). Columns J-O: Number of mapped reads per gene for each one of the three biological replicates per strain. Columns P-AC: Output from DESeq2 for WT vs. perRA mutant strains cultivated in DMCs (3 biological replicates per strain). Column P: Mean DESeq2 values for each gene. Column Q: Log2-fold change in gene expression. Column R: Power function transformation of log2-fold change. Column S: Fold regulation. Column T-W. Statistical analysis of differential gene expression including standard error estimate for the log2-fold change estimate (lfcSE, column T) and adjusted p-value (W). Columns X-AC: Normalized copy numbers per gene (3 biological replicates per strain). (XLSX)