RNA-seq data set.

Tab 1 shows the raw counts. Raw sequencing reads have been deposited at Gene Expression Omnibus (GEO) database under series ID GSE179103. A total of 42 to 57 million sequence reads were generated from each sample. Tab 2 shows transcripts per million (TPM). All genes with mapped reads were reported as TPM and a threshold TPM value of 10 was used as a cut-off to distinguish gene expression from background. Tab 3 shows differential sequence analysis via DESeq2 v1.30.1. Tab 4 shows genes that were deemed differentially expressed (adjusted p-value of 0.05 or below). Tab 5 and Tab 6 shows the expression profiles of “up cytosol” and “up vacuole” genes that passed statistical significance in 22 distinct infection-relevant in vitro growth conditions plus in macrophages (http://bioinf.gen.tcd.ie/cgi-bin/salcom.pl?db=salcom_mac_HL). (XLSX)