Differential gene expression results.

Sheets 1–4: Ranked lists of genes which passed the thresholds of log2(fold change) greater than or equal to 1 (corresponding to a fold change of 2) and p value less than or equal to 0.05 after false discovery rate (FDR) adjustment for multiple testing. Sheets are as follows: TS_up, TS_down–genes which are significantly more (up) or less (down) transcribed in infected samples compared to mock, TE_up, TE_down–genes which are significantly more (up) or less (down) efficiently translated in infected samples compared to mock. Read counts for each sample, normalised by the total number of host-mRNA-mapping reads for that sample, are given in the right-most columns. Sheets 5 and 6: Full lists of genes which pass the threshold for inclusion in the analyses (requires ten reads mapping to this gene between all samples). TS = transcription, TE = translation efficiency. (XLSX)