Additional file 1 of Differential lung gene expression changes in C57BL/6 and DBA/2 mice carrying an identical functional Mx1 gene reveals crucial differences in the host response

Additional file 1. Description of data: list of DEGs from comparison of infected B6-Mx1r/r at day 3 p.i. versus B6-Mx1r/r mock controls

Human β-actin DNA concentration in staff- and self-collected swabs.

<p>A. Human β-actin DNA concentration in staff- and self-collected swabs obtained according to the time scheme shown in Fig. 1. β-actin DNA concentration was determined by real-time PCR and is plotted on the y-axis as the number of molecules per swab. Boxes: upper border, 75^th percentile; lower border, 25^th percentile; bold horizontal line, median; whiskers, minimum and maximum excluding outliers (circles); circles, outlying values exceeding the 75^th percentile by >1.5 times the height of the box. B. β-actin DNA concentration per swab in relation to time elapsed between onset of ARI symptoms and the day of swabbing (r² = 0.02, p = 0.32).</p

Viral respiratory pathogens detected in staff-and self-collected swabs obtained in the study center¹.

1<p>Values represent the percentages of pairs of staff- and self-collected swabs obtained in the study center (total n = 75 swab pairs, collected from 56 participants) in which a given pathogen was detected by real-time PCR in at least one swab.</p

Relation between β-actin DNA concentration and viral positivity status in staff- and self-collected swabs collected on the same day.

<p>Analysis based on the data set used for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048508#pone-0048508-g002" target="_blank">Figure 2</a>, but stratified according to viral detection status (+ positive, − negative). Y-axis: human β-actin DNA molecules per swab. P values: p = 0.186 for comparison between negative and positive staff-swabs; p = 0.404 for comparison between negative and positive self-swabs (Wilcoxon rank sum test).</p

Agreement in pathogen detection between staff- and self-swabs collected on the same day.

<p>Swabs were designated positive if any of 15 respiratory viral pathogens were detected by real-time PCR (Seeplex RV15 ACE Detection kit, Seegene Germany, Eschborn, Germany). Concordant scenarios are shown on the left, discordant scenarios on the right.</p

Acceptability of nasal swabbing.

*<p>only those participants who collected at least one nasal swab.</p>**<p>all participants.</p

Timeline of staff-collected (interrupted line) and self-collected (solid line) swabs.

<p>A staff-collected and a self-collected swab were obtained on day 1 from separate nostrils. The participants were instructed to collect a self-swab from each nostril the next day, but the actual day of self-swabbing ranged from day 2 to day 6, as indicated by the triangle.</p

Additional file 1: Figure S1. of Lst1 deficiency has a minor impact on course and outcome of the host response to influenza A H1N1 infections in mice

Targeting and genotyping strategy of the Lst1 KO strain. Mice were genotyped by using different primer pairs leading to PCR products which allowed the identification of wild-type (310 bp), KO (400 bp) and heterozygous animals (310 bp and 400 bp) (A). Primers (blue arrows) used for genotyping: Lst1-fwd: 5′ - GTG CGT GCT CAG TCA CAC TA – 3′; Lst1-rev: 3′ - AGG CCA ACA ATA AGT CCT TAC – 5′; neofwd: 3′ - TCA TTC TCA GTA TTG TTT TGC C – 5′. Abbreviations: lacZ: ß-galactosidase coding sequence from the E.coli lacZ gene, hubiP: promoter from the human ubiquitin C gene, neor: coding sequence for neomycin phosphotransferase, p(A): polyadenylation signal, black arrow: direction of gene transcription, black boxes: Lst1 coding region. To confirm the knock-out of the Lst1 gene in C57BL/6 N-Lst1tm1(KOMP)Vlcg mice we performed reverse transcription. Figure S2. No difference in changes of body weight or survival rate between Lst1 KO and C57BL/6 J mice after infection with H3N2 influenza A virus Male C57BL/6 N-Lst1 tm1(KOMP)Vlcg (n = 7) and C57BL/6 J mice (n = 10) were infected intranasally with 2x10³ FFU H3N2 virus (A/HK/01/68) in 20 μl PBS. Body weight (A) and survival (B) were determined for each day p.i. for a period of 14 days. Percent weight change is shown with reference to the starting body weight. Significances were calculated using non-parametric Mann Whitney U test. (p < 0.01 for day 1) and Logrank test for survival rates (not significant). (PDF 230 kb

Nonparametric Spearman correlation coefficient was calculated for viral load in the lung and granulocyte to lymphocyte ratio in the blood using data sets from seven infection models: C57BL/6J: PR8M 2×10³ FFU and 2×10⁵ FFU, PR8F 2×10³ FFU, hvPR8 2×10³ FFU; DBA/2J: PR8M, PR8F, hvPR8 all 2×10³ FFU (see Figure I in File S1 and [21]).

<p>Nonparametric Spearman correlation coefficient was calculated for viral load in the lung and granulocyte to lymphocyte ratio in the blood using data sets from seven infection models: C57BL/6J: PR8M 2×10³ FFU and 2×10⁵ FFU, PR8F 2×10³ FFU, hvPR8 2×10³ FFU; DBA/2J: PR8M, PR8F, hvPR8 all 2×10³ FFU (see Figure I in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103149#pone.0103149.s001" target="_blank">File S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103149#pone.0103149-Blazejewska1" target="_blank">[21]</a>).</p

Pair wise statistical comparison of all granulocyte to lymphocyte ratios of C57BL/6J presented in Figure 2A.

<p>Data were analyzed for statistically significant differences using non-parametric Mann-Whitney-U-test. *: p-value<0.05; **: p-value<0.01; ***: p-value<0.001; ****: p-value<0.0001.</p