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Supplemental Materials The infection-tolerant mammalian reservoir of Lyme disease and other zoonoses broadly counters the inflammatory effects of endotoxin Supplemental Materials Figures S1-S5 Tables S1-S20 Figure S1. Digital photograph of two adult Peromyscus leucopus with exudative conjunctivitis and huddled together. The animals had received 10 mg/gm body of Escherichia coli lipopolysaccharide intraperitoneally the day before. Figure S2. Species- and tissue-specific responses to LPS. Independent differential gene expression analysis of RNA-seq data were performed for blood, spleen, and liver tissues of P. leucopus and M. musculus collected 4 h after injection with LPS or buffer alsone as control. These are represented as volcano plots with range- adjusted scales for the log2-transformed fold-changes on x-axes and log10-transformed FDR p values on y- axes. Colors of symbols denote the following: red, up-regulated gene with absolute fold-change > 4.0 and p value < 0.05; purple, down-regulated gene with absolute fold-change > 4.0 and p value < 0.05; and gray, all others. Numbers at the top left and right corners in each plot respresent numbers of down- and up-regulated genes, respectively. Figure 3 is same data with constant scales for x- and y-axes across the plots. Numerical values for each gene in the 6 datasets are provided in Tables S4-S9. Figure S3. Correlation of IL-10 and IL-10 P. leucopus and M. musculus from RNA-seq of spleen and of Figure 6B and TaBle S14. The scatter plot is log10 values of normalized unique reads of one coding sequence against another for each of the four groups, as defined in the legend for Figure 6 and indicated By different symBols. 4.0 3.0 2.0 Interleukin-12 MC ML PC PL 1.0 1.0 2.0 3.0 4.0 5.0 Interleukin-10 Figure S4. Assessment of diversity among individual animals by species in transcriptional responses to LPS for 17 genes. Pairwise coefficients of determination (R2) were calculated for the 66 intraspecies pairs for LPS-treated P. leucopus, the 66 intraspecies pairs for LPS-treated M. musculus, and the 144 interspecies pairs for all LPS-treated animals. Data were drawn from selective RNA-seq for the spleen (Table S14). The top panel is a frequency distribution of R2 values for all 3 sets of determinations. The bottom panel shows just the distributions of intraspecies pairwise determinations. Peromyscus Peromyscus Mus Mus 0.5 0.6 0.7 0.8 0.9 1.0 Pairwise R2 values Mus Peromyscus 1.00 0.95 values 2 R 0.90 0.85 Pairwise 0.80 30 20 10 0 10 20 30 Count Count Figure S5. DEGs of RNA-seq of selected protein coding sequences for blood or spleen samples from P. leucopus of > 1 year of age. The figure comprises 9 box-plots for representative genes, singly or in pairs. The x-axes indicate the treatment groups: control or LPS-treated. The y-axes are log10-transformed, normalized unique reads per coding sequence. Data values by individual coding sequence are given in Table S13. 5.0 5.0 5.0 Blood Blood Blood 4.0 4.0 4.5 3.0 3.0 dehydrogenase 4.0 2.0 3-P 2.0 3.5 1.0 Nitric oxide synthas 2 Arginase 1 0.0 1.0 3.0 Control LPS Glyceraldehyde Control LPS Transforming growh factor β Control LPS Secretory leukoycte peptidase inhib. Integrin binding sialoprotein 5.0 5.0 4.0 Blood Spleen Spleen 4.0 β 4.0 3.0 3.0 3.0 2.0 nterleukin-1 Interleukin-6 Interleukin-10 I Tumor necrosis factor IL-1 receptor antagonist Superoxide dismutase 2 2.0 2.0 1.0 Control LPS Control LPS Control LPS 4.0 4.0 5.0 Spleen Spleen Spleen 3.0 3.0 4.0 2.0 2.0 -deoxygenase 1 3.0 1.0 2,3 CCL2 CXCL11 1.0 2.0 0.0 Colony stimulating factor 2 0.0 Colony stimulating factor 3 1.0 Indoleamine Control LPS Control LPS Pentraxin 3 Control LPS Table S1. Line listing of animals by species and other characteristics for two LPS experiments Microbiome Age Conjunc- Cortico- Nitric Species Animal Group Sex Mass (g) Specimens alpha (weeks tivitis sterone oxide diversity 22275 Control F 15 20 - bld, liv, spl 3.49 254 17.3 22277* Control F 15 14 - bld, liv, spl 3.18 238 1.1 22282 Control F 14 15 - bld, liv, spl 3.51 21 nd 22279 Control F 15 15 - bld, liv, spl 3.50 78 3.9 22321 Control M 13 16 - bld, liv, spl 3.49 214 9.8 22335 Control M 12 17 - bld, liv, spl 3.42 84 7.8 22341 Control M 11 15 - bld, liv, spl 3.80 100 3.7 22315 Control M 13 20 - bld, liv, spl 3.83 497 nd Peromyscus 22258 LPS F 17 26 - bld, liv, spl 3.54 681 7.7 leucopus 22281 LPS F 15 21 + bld, liv, spl 3.61 748 10.2 22278* LPS F 15 17 + bld, liv, spl 3.31 740 11.5 22289 LPS F 15 15 - bld, liv, spl 3.62 642 nd 22292 LPS F 15 20 - bld, liv, spl 3.69 817 0.0 22284 LPS F 15 15 + bld, liv, spl 3.69 671 0.0 22319 LPS M 13 18 - bld, liv, spl 3.76 697 2.7 22316 LPS M 13 21 + bld, liv, spl 3.74 713 14.7 22325 LPS M 12 27 - bld, liv, spl 3.73 697 nd 22332 LPS M 12 25 - bld, liv, spl 3.40 658 nd 22327 LPS M 12 15 + bld, liv, spl 3.77 664 4.7 22339 LPS M 11 20 + bld, liv, spl 3.87 658 11.3 102 Control F 10 20 - bld, liv, spl 3.68 nd nd 120 Control F 10 20 - bld, liv, spl 3.52 21 7.8 F1_01 Control F 10 20 - bld, liv, spl 3.65 159 4.5 F3_02 Control F 10 19 - bld, liv, spl 3.65 109 2.7 106 Control M 12 24 - bld, liv, spl 3.67 34 20.7 115 Control M 12 26 - bld, liv, spl 3.59 137 4.7 116 Control M 12 29 - bld, liv, spl 3.57 38 3.7 Mus M4_04 Control M 12 31 - bld, liv, spl 3.62 40 7.8 musculus 101 LPS F 10 19 - bld, liv, spl 2.98 709 52.1 103 LPS F 10 21 - bld, liv, spl 3.57 699 45.6 104 LPS F 10 20 - bld, liv, spl 3.14 662 29.3 105 LPS F 10 19 - bld, liv, spl 3.47 647 42.6 118 LPS F 10 18 - bld, liv, spl 3.63 709 18.3 F3_03 LPS F 10 21 - bld, liv, spl 3.65 687 23.5 107 LPS M 12 29 - bld, liv, spl 3.69 566 8.1 108 LPS M 12 25 - bld, liv, spl 3.59 490 30.3 109 LPS M 12 29 - bld, liv, spl 3.70 634 25.5 M2_05 LPS M 12 27 - bld, liv, spl 3.66 587 12.2 M4_06 LPS M 12 28 - bld, liv, spl 3.62 518 nd M4_07 LPS M 12 30 - bld, liv, spl 3.62 577 2.5 20694 Control F 83 21 - spl nd nd nd 20713 Control F 73 23 - bld nd nd nd 20733† Control F 79 18 - spl nd nd nd 20807# Control F 69 18 - spl nd nd nd 20949 Control F 54 19 - spl nd nd nd 20495 Control M 93 22 - bld, spl nd nd nd Peromyscus 20613 Control M 84 22 - bld nd nd nd leucopus 20688 LPS F 83 18 + spl nd nd nd 20695 LPS F 83 25 - spl nd nd nd 20696 LPS F 74 18 - bld nd nd nd 20702# LPS F 83 17 - spl nd nd nd 20704 LPS F 74 19 - bld nd nd nd 20732† LPS F 71 23 - bld, spl nd nd nd 20819 LPS F 69 28 + spl nd nd nd 20483 LPS M 94 23 - bld, spl nd nd nd 20501 LPS M 93 24 - bld nd nd nd * Mating pair H-106, same litter † Mating pair H-1056, same litter # Mating pair H-1055, different litter Table S2 Table S2. Pathway enrichments from metabolomics of plasma of Peromyscus leucopus and Mus musculus with or without LPS treatment Pathway Pathway Mus hits Mus Mus Mus Mus p Peromyscus Peromyscus Peromyscus Peromyscus Peromyscus total significant expected enriched value hits significant expected enriched p value Mus KEGG hits Peromyscus KEGG hits Alanine, aspartate and glutamate metabolism 28 25 17 8.66 1.96 6.7E-04 25 15 12.30 1.22 2.0E-01 C01042;C02362;C00049;C00152;C00402; C01042;C02362;C00049;C00152; C03406;C00041;C00232;C00025;C03912; C00402;C00041;C00232;C00025; C20776;C00158;C00438;C00026;C00169; C00334;C00064;C20776;C00158; C00352;C03090 C00026;C00352;C03090 alpha-Linolenic acid metabolism 12 11 4 3.71 1.08 5.7E-01 11 2 5.27 0.38 9.9E-01 C16331;C16327;C06427;C16336;C16300 C06427;C16300 Amino sugar and nucleotide sugar metabolism 35 28 4 10.82 0.37 1.0E+00 35 13 15.37 0.85 9.5E-01 C06241;C00270;C00352;C00190 C00357;C04501;C00270;C00029; C00352;C00267;C00984;C01019; C03410;C00461;C00159;C02336; C00329;C04257;C00052;C03691 Aminoacyl-tRNA biosynthesis 22 21 11 6.80 1.62 7.4E-02 21 18 9.66 1.86 6.2E-04 C00152;C00135;C00079;C00049;C00065; C00152;C00079;C00062;C00064; C00073;C00183;C00041;C00078;C00148; C00037;C00049;C00065;C00073; C00025 C00183;C00041;C00047;C00407; C00123;C00188;C00078;C00082; C00148;C00025 Arachidonic acid metabolism 35 35 4 10.82 0.37 1.0E+00 35 13 15.37 0.85 9.5E-01 C00219;C05956;C02166;C05951 C14768;C14769;C14770;C14771; C00219;C14781;C14813;C05966; C05356;C05956;C00909;C02165; C00427;C00584;C14782;C14814; C14778;C14823;C14812;C14748; C04742;C14749;C04805;C05965; C04853;C01312;C02198;C00696; C00639 Arginine and proline metabolism 37 35 10 11.44 0.87 8.4E-01 35 21 16.25 1.29 1.4E-01 C05933;C00300;C00019;C00763;C05946; C00062;C00334;C00019;C00315; C05938;C00148;C03912;C03287;C00025; C02714;C05936;C00750;C05147; C00077 C00763;C05947;C05938;C04281; C01157;C00148;C03440;C03287; C00025;C01165;C00077;C02946; C04282 Arginine biosynthesis 14 13 9 4.33 2.08 1.2E-02 13 9 6.15 1.46 1.3E-01 C00025;C03406;C00327;C00049;C00169; C00025;C00062;C00437;C00327; C00077;C00026;C00624;C00086 C00049;C00077;C00064;C00026; C00624 Ascorbate and aldarate metabolism 10 9 2 3.09 0.65 8.8E-01 9 4 4.39 0.91 7.4E-01 C01040;C00191;C00800 C01040;C00137;C00029;C00191; C00800;C00818 beta-Alanine metabolism 21 16 5 6.49 0.77 7.1E-01 16 8 9.22 0.87 5.9E-01 C00099;C00049;C02642;C05341;C00135 C00083;C00099;C00049;C02642; C00386;C00750;C05341;C00315 Biosynthesis of unsaturated fatty acids 34 27 7 10.51 0.67 8.9E-01 27 10 14.94 0.67 9.4E-01 C01595;C00219;C03242;C06426;C06429; C00249;C01530;C00712;C01595; C06428;C06427 C00219;C03242;C06426;C06429; C06428;C06427 Biotin metabolism 4 4 1 1.24 0.81 8.2E-01 4 4 1.76 2.28 6.1E-02 C00120 C00120;C05921;C05552;C00047 Butanoate metabolism 15 14 8 4.64 1.72 7.3E-02 13 8 6.59 1.21 2.8E-01 C01089;C00164;C00332;C00025;C00232; C01089;C00164;C00334;C00025; C00246;C00026;C02630 C00232;C00246;C00026;C02630 Caffeine metabolism 12 12 4 3.71 1.08 6.5E-01 12 7 5.27 1.33 3.8E-01 C13747;C07480;C16359;C16360;C16356;
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