fda_rna_seq_og_lissal

1−1_trial5_water_lis 1−2_trial1_chlorine_lis 10_trial2_water−ultrasound_lis 11_trial3_water−ultrasound_lis 12_trial4_water−ultrasound_lis 13_trial1_chlorine−ultrasound_lis 14_trial2_chlorine−ultrasound_lis 15_trial3_chlorine−ultrasound_lis 16_trial4_chlorine−ultrasound_lis 2−1_trial6_water_lis 2−2_trial2_chlorine_lis 3−1_trial7_water_lis 3−2_trial3_chlorine_lis 4−1_trial8_water_lis 4−2_trial4_chlorine_lis 9_trial1_water−ultrasound_lis 0e+00 2e+06 4e+06 6e+06 # read pairs Sample variable protein_coding tRNA rRNA SRP_RNA ncRNA RNase_P_RNA tmRNA missing 1−1_trial5_water_lis 1−2_trial1_chlorine_lis 10_trial2_water−ultrasound_lis 11_trial3_water−ultrasound_lis 12_trial4_water−ultrasound_lis 13_trial1_chlorine−ultrasound_lis 14_trial2_chlorine−ultrasound_lis 15_trial3_chlorine−ultrasound_lis 16_trial4_chlorine−ultrasound_lis 2−1_trial6_water_lis 2−2_trial2_chlorine_lis 3−1_trial7_water_lis 3−2_trial3_chlorine_lis 4−1_trial8_water_lis 4−2_trial4_chlorine_lis 9_trial1_water−ultrasound_lis 0e+00 2e+06 4e+06 6e+06 # read pairs Sample variable protein_coding nonprot 1−1_trial5_water_lis 1−2_trial1_chlorine_lis 10_trial2_water−ultrasound_lis 11_trial3_water−ultrasound_lis 12_trial4_water−ultrasound_lis 13_trial1_chlorine−ultrasound_lis 14_trial2_chlorine−ultrasound_lis 15_trial3_chlorine−ultrasound_lis 16_trial4_chlorine−ultrasound_lis 2−1_trial6_water_lis 2−2_trial2_chlorine_lis 3−1_trial7_water_lis 3−2_trial3_chlorine_lis 4−1_trial8_water_lis 4−2_trial4_chlorine_lis 9_trial1_water−ultrasound_lis 0.00 0.25 0.50 0.75 1.00 Proportion of reads Sample variable protein_coding nonprot A BC Supplemental Figure S1. Bar plots showcasing read mapping statistics (X-axis) for each Listeria monocytogenes sample (Y-axis). Plots denote: (A) the total number of read pairs assigned to each feature type (including unassigned read pairs, denoted as “missing”); (B) the total number of read pairs assigned to protein-coding features (“protein_coding”, blue) versus everything else (“nonprot”, pink); (C) the proportion of read pairs per sample assigned to protein-coding features (“protein_coding”, blue) versus everything else (“nonprot”, pink). 1−1_trial1_water_sal_trimmed 1−2_trial1_chlorine_sal_trimmed 1−3_trial1_water−ultrasound_sal_trimmed 1−4_trial1_chlorine−ultrasound_sal_trimmed 2−1_trial2_water_sal_trimmed 2−2_trial2_chlorine_sal_trimmed 2−3_trial2_water−ultrasound_sal_trimmed 2−4_trial2_chlorine−ultrasound_sal_trimmed 3−1_trial3_water_sal_trimmed 3−2_trial3_chlorine_sal_trimmed 3−3_trial3_water−ultrasound_sal_trimmed 3−4_trial3_chlorine−ultrasound_sal_trimmed 4−1_trial4_water_sal_trimmed 4−2_trial4_chlorine_sal_trimmed 4−3_trial4_water−ultrasound_sal_trimmed 4−4_trial4_chlorine−ultrasound_sal_trimmed 0e+00 2e+06 4e+06 6e+06 # read pairs Sample variable protein_coding rRNA tRNA SRP_RNA ncRNA tmRNA other misc_RNA missing 1−1_trial1_water_sal_trimmed 1−2_trial1_chlorine_sal_trimmed 1−3_trial1_water−ultrasound_sal_trimmed 1−4_trial1_chlorine−ultrasound_sal_trimmed 2−1_trial2_water_sal_trimmed 2−2_trial2_chlorine_sal_trimmed 2−3_trial2_water−ultrasound_sal_trimmed 2−4_trial2_chlorine−ultrasound_sal_trimmed 3−1_trial3_water_sal_trimmed 3−2_trial3_chlorine_sal_trimmed 3−3_trial3_water−ultrasound_sal_trimmed 3−4_trial3_chlorine−ultrasound_sal_trimmed 4−1_trial4_water_sal_trimmed 4−2_trial4_chlorine_sal_trimmed 4−3_trial4_water−ultrasound_sal_trimmed 4−4_trial4_chlorine−ultrasound_sal_trimmed 0e+00 2e+06 4e+06 6e+06 # read pairs Sample variable protein_coding nonprot 1−1_trial1_water_sal_trimmed 1−2_trial1_chlorine_sal_trimmed 1−3_trial1_water−ultrasound_sal_trimmed 1−4_trial1_chlorine−ultrasound_sal_trimmed 2−1_trial2_water_sal_trimmed 2−2_trial2_chlorine_sal_trimmed 2−3_trial2_water−ultrasound_sal_trimmed 2−4_trial2_chlorine−ultrasound_sal_trimmed 3−1_trial3_water_sal_trimmed 3−2_trial3_chlorine_sal_trimmed 3−3_trial3_water−ultrasound_sal_trimmed 3−4_trial3_chlorine−ultrasound_sal_trimmed 4−1_trial4_water_sal_trimmed 4−2_trial4_chlorine_sal_trimmed 4−3_trial4_water−ultrasound_sal_trimmed 4−4_trial4_chlorine−ultrasound_sal_trimmed 0.00 0.25 0.50 0.75 1.00 Proportion of reads Sample variable protein_coding nonprot A BC Supplemental Figure S2. Bar plots showcasing read mapping statistics (X-axis) for each Salmonella enterica sample (Y-axis). Plots denote: (A) the total number of read pairs assigned to each feature type (including unassigned read pairs, denoted as “missing”); (B) the total number of read pairs assigned to protein-coding features (“protein_coding”, blue) versus everything else (“nonprot”, pink); (C) the proportion of read pairs per sample assigned to protein-coding features (“protein_coding”, blue) versus everything else (“nonprot”, pink). 1−1_trial5_water_lis 1−2_trial1_chlorine_lis 10_trial2_water−ultrasound_lis 11_trial3_water−ultrasound_lis 12_trial4_water−ultrasound_lis 13_trial1_chlorine−ultrasound_lis 14_trial2_chlorine−ultrasound_lis 15_trial3_chlorine−ultrasound_lis 16_trial4_chlorine−ultrasound_lis 2−1_trial6_water_lis 2−2_trial2_chlorine_lis 3−1_trial7_water_lis 3−2_trial3_chlorine_lis 4−1_trial8_water_lis 4−2_trial4_chlorine_lis 9_trial1_water−ultrasound_lis 0.00 0.25 0.50 0.75 1.00 Proportion of reads Sample variable Assigned Unassigned_Unmapped Unassigned_NoFeatures Unassigned_Ambiguity 1−1_trial5_water_lis 1−2_trial1_chlorine_lis 10_trial2_water−ultrasound_lis 11_trial3_water−ultrasound_lis 12_trial4_water−ultrasound_lis 13_trial1_chlorine−ultrasound_lis 14_trial2_chlorine−ultrasound_lis 15_trial3_chlorine−ultrasound_lis 16_trial4_chlorine−ultrasound_lis 2−1_trial6_water_lis 2−2_trial2_chlorine_lis 3−1_trial7_water_lis 3−2_trial3_chlorine_lis 4−1_trial8_water_lis 4−2_trial4_chlorine_lis 9_trial1_water−ultrasound_lis 0e+00 2e+06 4e+06 6e+06 # read pairs Sample A B Supplemental Figure S3. Bar plots showcasing read mapping statistics (X-axis) for each Listeria monocytogenes sample (Y-axis). Plots denote the (A) total and (B) proportion of read pairs assigned to each featureCounts category. 1−1_trial1_water_sal_trimmed 1−2_trial1_chlorine_sal_trimmed 1−3_trial1_water−ultrasound_sal_trimmed 1−4_trial1_chlorine−ultrasound_sal_trimmed 2−1_trial2_water_sal_trimmed 2−2_trial2_chlorine_sal_trimmed 2−3_trial2_water−ultrasound_sal_trimmed 2−4_trial2_chlorine−ultrasound_sal_trimmed 3−1_trial3_water_sal_trimmed 3−2_trial3_chlorine_sal_trimmed 3−3_trial3_water−ultrasound_sal_trimmed 3−4_trial3_chlorine−ultrasound_sal_trimmed 4−1_trial4_water_sal_trimmed 4−2_trial4_chlorine_sal_trimmed 4−3_trial4_water−ultrasound_sal_trimmed 4−4_trial4_chlorine−ultrasound_sal_trimmed 0.00 0.25 0.50 0.75 1.00 Proportion of reads Sample variable Assigned Unassigned_Unmapped Unassigned_NoFeatures Unassigned_Ambiguity 1−1_trial1_water_sal_trimmed 1−2_trial1_chlorine_sal_trimmed 1−3_trial1_water−ultrasound_sal_trimmed 1−4_trial1_chlorine−ultrasound_sal_trimmed 2−1_trial2_water_sal_trimmed 2−2_trial2_chlorine_sal_trimmed 2−3_trial2_water−ultrasound_sal_trimmed 2−4_trial2_chlorine−ultrasound_sal_trimmed 3−1_trial3_water_sal_trimmed 3−2_trial3_chlorine_sal_trimmed 3−3_trial3_water−ultrasound_sal_trimmed 3−4_trial3_chlorine−ultrasound_sal_trimmed 4−1_trial4_water_sal_trimmed 4−2_trial4_chlorine_sal_trimmed 4−3_trial4_water−ultrasound_sal_trimmed 4−4_trial4_chlorine−ultrasound_sal_trimmed 0e+00 2e+06 4e+06 6e+06 # read pairs Sample A B Supplemental Figure S4. Bar plots showcasing read mapping statistics (X-axis) for each Salmonella enterica sample (Y-axis). Plots denote the (A) total and (B) proportion of read pairs assigned to each featureCounts category. −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty 1.00 1.00 0.99 0.98 1.00 0.97 0.98 1.00 1.00 0.98 0.98 0.99 0.96 0.97 1.00 1.00 0.99 0.99 0.96 0.96 0.99 1.00 0.97 0.93 0.94 0.98 1.00 0.99 0.99 0.99 1.00 1.00 0.97 1.00 0.98 1.00 −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty A B CD Supplemental Figure S5. Correlation between Listeria monocytogenes RNA-seq dendrograms. Dendrograms were constructed using VST-transformed read counts, Euclidean distances, and one of eight linkage methods (red text). Plots were constructed using the corrplot function in R, using the (A) pie, (B) ellipse, (C) number, and (D) color methods. −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty 1.00 0.79 0.90 0.96 0.90 0.40 0.64 0.94 1.00 0.73 0.69 0.73 0.47 0.56 0.69 1.00 0.85 0.98 0.24 0.46 0.74 1.00 0.85 0.26 0.59 0.95 1.00 0.29 0.48 0.74 1.00 0.77 0.37 1.00 0.68 1.00 −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty −1−0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 Average Complete Centroid Median Single Ward Ward.D2 McQuitty Average Complete Centroid Median Single Ward Ward.D2 McQuitty Supplemental Figure S6. Correlation between Salmonella enterica RNA-seq dendrograms. Dendrograms were constructed using VST-transformed read counts, Euclidean distances, and one of eight linkage methods (red text). Plots were constructed using the corrplot function in R, using the (A) pie, (B) ellipse, (C) number, and (D) color methods. −2 −1 0 1 −2−10 12 umap_x umap_y chlorine chlorine not_chlorine −2 −1 0 1 −2−10 12 umap_x umap_y chlorine chlorine not_chlorine −2 −1 0 1 −2−10 1 2 umap_x umap_y group chlorine chlorine−ultrasound water water−ultrasound −2 −1 0 1 −2−10 1 2 umap_x umap_y group chlorine chlorine−ultrasound water water−ultrasound 1−1_trial5_water_lis 1−2_trial1_chlorine_lis 10_trial2_water−ultrasound_lis 11_trial3_water−ultrasound_lis 12_trial4_water−ultrasound_lis 13_trial1_chlorine−ultrasound_lis 14_trial2_chlorine−ultrasound_lis 15_trial3_chlorine−ultrasound_lis 16_trial4_chlorine−ultrasound_lis 2−1_trial6_water_lis 2−2_trial2_chlorine_lis 3−1_trial7_water_lis 3−2_trial3_chlorine_lis 4−1_trial8_water_lis 4−2_trial4_chlorine_lis 9_trial1_water−ultrasound_lis −2 −1 0 1 −2−10 1 2 umap_x umap_y log10(seqdepth) 6.2 6.3 6.4 6.5 6.6 6.7 −2 −1 0 1 −2−10 12 umap_x umap_y trial trial1 trial2 trial3 trial4 trial5 trial6 trial7 trial8 −2 −1 0 1 −2−10 12 umap_x umap_y trial trial1 trial2 trial3 trial4 trial5 trial6 trial7 trial8 −2 −1 0 1 −2−10 12 umap_x umap_y ultrasound not_ultrasound ultrasound −2 −1 0 1 −2−10 12 umap_x umap_y ultrasound not_ultrasound ultrasound −2 −1 0 1 −2−10 12 umap_x umap_y water not_water water −2 −1 0 1 −2−10 12 umap_x umap_y water not_water water Supplemental Figure S7. Listeria monocytogenes UMAPs, constructed using VST-transformed read counts as input, drawn (1) with and (2) without convex hulls. Points denote samples and are colored by the following: (A) treatment (“group”); whether samples were exposed to (B) ultrasound or not (“ultrasound”) or (C) chlorine or not (“chlorine”); (D) whether samples were water (control) samples or not (“water”); (E) trial (batch); (F) log10 sequencing depth. A1 A2 B1 B2 C1 C2 D1 D2 E1 E2 F −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 chlorine chlorine not_chlorine −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 chlorine chlorine not_chlorine PC3 −5 0 5 10 −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 group chlorine chlorine−ultrasound water water−ultrasound −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 group chlorine chlorine−ultrasound water water−ultrasound PC3 −5 0 5 10 1−1_trial5_water_lis 1−2_trial1_chlorine_lis 10_trial2_water−ultrasound_lis 11_trial3_water−ultrasound_lis 12_trial4_water−ultrasound_lis 13_trial1_chlorine−ultrasound_lis 14_trial2_chlorine−ultrasound_lis 15_trial3_chlorine−ultrasound_lis 16_trial4_chlorine−ultrasound_lis 2−1_trial6_water_lis 2−2_trial2_chlorine_lis 3−1_trial7_water_lis 3−2_trial3_chlorine_lis 4−1_trial8_water_lis 4−2_trial4_chlorine_lis 9_trial1_water−ultrasound_lis −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 log10(seqdepth) 6.2 6.3 6.4 6.5 6.6 6.7 PC3 a a a a −5 0 5 10 −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 trial trial1 trial2 trial3 trial4 trial5 trial6 trial7 trial8 −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 trial trial1 trial2 trial3 trial4 trial5 trial6 trial7 trial8 PC3 −5 0 5 10 −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 ultrasound not_ultrasound ultrasound −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 ultrasound not_ultrasound ultrasound PC3 −5 0 5 10 −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 water not_water water −30 −20 −10 0 10 20 −40 −20 0 20 PC1 PC2 water not_water water PC3 −5 0 5 10 Supplemental Figure S8. Principal component analysis (PCA) of Listeria monocytogenes VST-transformed read counts, drawn (1) with and (2) without convex hulls. Points denote samples and are colored by the following: (A) treatment (“group”); whether samples were exposed to (B) ultrasound or not (“ultrasound”) or (C) chlorine or not (“chlorine”); (D) whether samples were water (control) samples or not (“water”); (E) trial (batch); (F) log10 sequencing depth. PC1 (X-axis) and PC2 (Y-axis) are displayed in all plots; in plots without convex hulls, the size of each point denotes PC3. A1 A2 B1 B2 C1 C2 D1 D2 E1 E2 F −1 0 1 −10 1 umap_x umap_y chlorine chlorine not_chlorine −1 0 1 −10 1 umap_x umap_y chlorine chlorine not_chlorine −1 0 1 −10 1 umap_x umap_y group chlorine chlorine−ultrasound water water−ultrasound −1 0 1 −10 1 umap_x umap_y group chlorine chlorine−ultrasound water water−ultrasound 1−1_trial1_water_sal_trimmed 1−2_trial1_chlorine_sal_trimmed 1−3_trial1_water−ultrasound_sal_trimmed 1−4_trial1_chlorine−ultrasound_sal_trimmed 2−1_trial2_water_sal_trimmed 2−2_trial2_chlorine_sal_trimmed 2−3_trial2_water−ultrasound_sal_trimmed 2−4_trial2_chlorine−ultrasound_sal_trimmed 3−1_trial3_water_sal_trimmed 3−2_trial3_chlorine_sal_trimmed 3−3_trial3_water−ultrasound_sal_trimmed 3−4_trial3_chlorine−ultrasound_sal_trimmed 4−1_trial4_water_sal_trimmed 4−2_trial4_chlorine_sal_trimmed 4−3_trial4_water−ultrasound_sal_trimmed 4−4_trial4_chlorine−ultrasound_sal_trimmed −1 0 1 −1 0 1 umap_x umap_y log10(seqdepth) 5.0 5.5 6.0 6.5 −1 0 1 −1 0 1 umap_x umap_y trial trial1 trial2 trial3 trial4 −1 0 1 −1 0 1 umap_x umap_y trial trial1 trial2 trial3 trial4 −1 0 1 −10 1 umap_x umap_y ultrasound not_ultrasound ultrasound −1 0 1 −10 1 umap_x umap_y ultrasound not_ultrasound ultrasound −1 0 1 −10 1 umap_x umap_y water not_water water −1 0 1 −10 1 umap_x umap_y water not_water water Supplemental Figure S9. Salmonella enterica UMAPs, constructed using VST-transformed read counts as input, drawn (1) with and (2) without convex hulls. Points denote samples and are colored by the following: (A) treatment (“group”); whether samples were exposed to (B) ultrasound or not (“ultrasound”) or (C) chlorine or not (“chlorine”); (D) whether samples were water (control) samples or not (“water”); (E) trial (batch); (F) log10 sequencing depth. A1 A2 B1 B2 C1 C2 D1 D2 E1 E2 F