Volume 14, Issue 6, Pages 683-695 (December 2013) An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium  Carsten Kröger, Aoife Colgan, Shabarinath Srikumar, Kristian Händler, Sathesh K. Sivasankaran, Disa L. Hammarlöf, Rocío Canals, Joe E. Grissom, Tyrrell Conway, Karsten Hokamp, Jay C.D. Hinton  Cell Host & Microbe  Volume 14, Issue 6, Pages 683-695 (December 2013) DOI: 10.1016/j.chom.2013.11.010 Copyright © 2013 Elsevier Inc. Terms and Conditions

Figure 1 Visualization of the Extent of Gene Expression Changes and Comparison of the Upregulated Genes that Respond to Brief Environmental Shocks (A–D) The size of the area of the outer circles corresponds to the number of genes which are > 3-fold up- and downregulated in comparison to MEP (A) (cold shock, 109 genes; LowFe2+, 109 genes; NaCl shock, 737 genes; anaerobic shock, 951 genes; bile shock, 245 genes; pH3 shock, 465 genes; pH 5.8 shock, 134 genes) and InSPI2 (B) (NonSPI2, 354 genes; LowMg2+, 328 genes; nitric oxide shock, 737 genes; peroxide shock, 1,334 genes). The size of the area of each central comparator circle corresponds to the number of genes that are expressed (TPM > 10), and these are MEP (3,008 genes) and InSPI2 (3,134 genes). The Venn diagrams show the number of genes that are > 3-fold upregulated in the environmental shocks in comparison to MEP (C) and InSPI2 (D). The Venn diagrams were created using Venny (http://bioinfogp.cnb.csic.es/tools/venny/). See also Data Set S2. Cell Host & Microbe 2013 14, 683-695DOI: (10.1016/j.chom.2013.11.010) Copyright © 2013 Elsevier Inc. Terms and Conditions

Figure 2 Classification of Transcriptional Start Sites of S. Typhimurium (A) The identified TSS were grouped into nine promoter categories according to Sharma et al. (2010). (B) Mapped sequence reads for the narK and STnc2040 genes presented in the IGB browser. The scale is 0–100 normalized reads for every sample. The figure shows the TSS of narK, which is only expressed in anaerobic shock and is present in the pool. (C) TSS distribution from five dRNA-seq experiments (MEP, ESP, LSP, InSPI2, and RNA pool). See also Data Set S3. Cell Host & Microbe 2013 14, 683-695DOI: (10.1016/j.chom.2013.11.010) Copyright © 2013 Elsevier Inc. Terms and Conditions

Figure 3 Visualization of Mapped Sequence Reads in the SPI1 Pathogenicity Island Protein coding gene names are labeled in black, small RNA gene names in blue. TSS are marked by arrows. All dRNA-seq libraries are shown in red. The figure was prepared with the IGB browser, and the scale is 0–100 normalized reads for every sample. See also Figure S2. Cell Host & Microbe 2013 14, 683-695DOI: (10.1016/j.chom.2013.11.010) Copyright © 2013 Elsevier Inc. Terms and Conditions

Figure 4 Absolute Gene Expression for SPI1 and SPI2 The heat map shows the absolute gene expression of SPI1 (left) and SPI2 (right) genes in TPM values. Coding gene names are labeled in black, small RNA gene names in blue. The TPM values are in Data Set S2. See also Figure S5. Cell Host & Microbe 2013 14, 683-695DOI: (10.1016/j.chom.2013.11.010) Copyright © 2013 Elsevier Inc. Terms and Conditions

Figure 5 Absolute and Relative Expression of Genes Encoding Effector Proteins Genes that encode proteins translocated by the SPI1 or SPI2 T3SS, or both, are labeled in orange (SPI1), green (SPI2), and black (both), respectively (Buckner et al., 2011; Figueira et al., 2013; Heffron et al., 2011). See also Data Set S2. Cell Host & Microbe 2013 14, 683-695DOI: (10.1016/j.chom.2013.11.010) Copyright © 2013 Elsevier Inc. Terms and Conditions

Figure 6 Expression Analyses and Classification of sRNAs of S. Typhimurium (A) Expression of six small RNAs: DapZ, OxyS, RybB, RprA, RyhB-1, and InvR. The pie charts show the proportion of sRNA gene expression across different conditions (based on TPM values). (B) Northern blots of two sRNAs (STnc3120, STnc3080). STnc3120 is upregulated in response to NaCl shock, while STnc3080 is upregulated upon LowFe2+ shock. 5S rRNA served as a loading control. (C) Genomic location of sRNAs relative to coding genes. The height of each bar reflects the number of sRNAs in each category (Data Set S4). (D) Hfq binding of sRNAs in the context of their genomic location. Hfq binding was assessed using the Hfq-coIP data produced by Chao et al. (2012) and Sittka et al. (2008) (Data Set S4). A selection of sRNAs reported to bind Hfq is shown in the figure. (E) Assessment of sRNA transcripts. Based on enrichment in the dRNA-seq experiments, the bar chart shows the number of sRNAs that are unequivocally primary transcripts in the context of their genomic location (red proportion of each bar). See also Figure S7. Cell Host & Microbe 2013 14, 683-695DOI: (10.1016/j.chom.2013.11.010) Copyright © 2013 Elsevier Inc. Terms and Conditions