S1 Tab: Differentially expressed genes identified in naïve, female vs male alveolar macrophages.

The table shows those DEGs identified in female vs male (A) wild type or (B) HRB-Mertk-/- alveolar macrophage transcriptomes. No downregulated genes were identified. Asterisks indicate those genes identified in both genotypes. S2 Tab: Differentially expressed genes identified in female, HRB-Mertk-/- vs wild type alveolar macrophages. Comparison of naïve, HRB-Mertk-/- vs wild type alveolar macrophages isolated from female mice. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change (Column J). S3 Tab: Differentially expressed genes identified in male, HRB-Mertk-/- vs wild type alveolar macrophages. Comparison of naïve, HRB-Mertk-/- vs wild type alveolar macrophages isolated from male mice. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change (Column J). S4 Tab: Gene ontology terms identified by functional enrichment analysis of HRB-Mertk-/- vs wild type alveolar macrophages. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in HRB-Mertk-/- vs wild type alveolar macrophages. The table list those gene ontology terms enriched in HRB-Mertk-/- vs wild type alveolar macrophage transcriptomes (adjPval <  0.05). Pathways are organized by normalized enrichment score, NES. S5 Tab: Gene ontology terms identified by gene list over-representation analysis of DEGs in each k-means cluster comparing HRB-Mertk-/- vs wild type alveolar macrophages. k-means clustering analysis was performed on DEGs that changed>  ± 1.5-fold in HRB-Mertk-/- alveolar macrophages. The analysis resulted in 4 clusters. Gene list over-representation analysis using DEGs was performed within each cluster. The table list the statistically significant GO terms enriched in (A) cluster 1 (rows 3-21) and (B) cluster 4 (rows 24-43). No GO terms were identified in clusters 2 or 3. GO pathways are organized by adjusted p value (padj). The number of DEGs (overlap) identified in HRB-Mertk-/- alveolar macrophages and their gene symbols (overlap genes) associated with each GO pathway are listed. (C) The DEGs used to perform k-means analysis and the clusters they were associated with are listed in column A. S6 Tab: Differentially expressed genes identified in unstimulated, HRB-Mertk-/- vs wild type alveolar macrophages ex vivo. Comparison of unstimulated, ex vivo alveolar macrophages isolated from HRB-Mertk-/- or wild type mice. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. S7 Tab: Differentially expressed genes identified in S. pneumoniae stimulated, HRB-Mertk-/- vs wild type alveolar macrophages ex vivo. Comparison of S. pneumoniae stimulated, ex vivo alveolar macrophages isolated from HRB-Mertk-/- or wild type mice. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. S8 Tab: Gene ontology terms identified by functional enrichment analysis of S. pneumoniae stimulated, HRB-Mertk-/- vs wild type alveolar macrophages ex vivo. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in S. pneumoniae stimulated HRB-Mertk-/- vs wild type ex vivo alveolar macrophages. The table list those gene ontology terms enriched in stimulated Mertk-/- vs wild type alveolar macrophage transcriptomes (adjPval <  0.05). Pathways are organized by normalized enrichment score, NES. S9 Tab: Differentially expressed genes identified in HRB-Mertk-/-, S. pneumoniae stimulated vs unstimulated alveolar macrophages ex vivo. Comparison of S. pneumoniae stimulated vs unstimulated HRB-Mertk-/- alveolar macrophages. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. S10 Tab: Differentially expressed genes identified in wild type, S. pneumoniae stimulated vs unstimulated alveolar macrophages ex vivo. Comparison of S. pneumoniae stimulated vs unstimulated wild type alveolar macrophages. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. S11 Tab: Gene ontology terms identified by functional enrichment analysis of HRB-Mertk-/-, S. pneumoniae stimulated vs unstimulated alveolar macrophages ex vivo. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in S. pneumonia stimulated HRB-Mertk-/- alveolar macrophages compared to unstimulated cells. The table list those gene ontology terms enriched in stimulated HRB-Mertk-/- alveolar macrophage transcriptomes (adjPval <  0.05). Pathways similarly identified in stimulated vs unstimulated, wild type alveolar macrophages (S12 Tab) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-132). Pathways uniquely identified in S. pneumoniae stimulated HRB-Mertk-/- alveolar macrophages are listed in rows 145-529. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 134-142) describes those functional categories. S12 Tab: Gene ontology terms identified by functional enrichment analysis of wild type, S. pneumoniae stimulated vs unstimulated alveolar macrophages ex vivo. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in S. pneumonia stimulated wild type alveolar macrophages compared to unstimulated cells. The table list those gene ontology terms enriched in stimulated wild type alveolar macrophage transcriptomes (adjPval <  0.05). Pathways similarly identified in stimulated vs unstimulated, HRB-Mertk-/- alveolar macrophages (S11 Tab in S2 File) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-132). Pathways uniquely identified in S. pneumoniae stimulated wild type alveolar macrophages are listed in rows 144-189. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 134-142) describes those functional categories. S13 Tab: Reactome pathways identified by functional enrichment analysis of HRB-Mertk-/-, S. pneumoniae stimulated vs unstimulated alveolar macrophages ex vivo. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in S. pneumonia stimulated HRB-Mertk-/- alveolar macrophages compared to unstimulated cells. The table list those Reactome pathways enriched in stimulated HRB-Mertk-/- alveolar macrophage transcriptomes (adjPval <  0.05). Pathways similarly identified in stimulated vs unstimulated, wild type alveolar macrophages (Supplemental Table 14) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-43). Pathways uniquely identified in S. pneumoniae stimulated HRB-Mertk-/- alveolar macrophages are listed in rows 55-94. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 45-53) describes those functional categories. S14 Tab: Reactome pathway identified by functional enrichment analysis of wild type, S. pneumoniae stimulated vs unstimulated alveolar macrophages ex vivo. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in S. pneumonia stimulated wild type alveolar macrophages compared to unstimulated cells. The table list those Reactome pathways enriched in stimulated wild type alveolar macrophage transcriptomes (adjPval <  0.05). Pathways similarly identified in stimulated vs unstimulated, HRB-Mertk-/- alveolar macrophages (S13 Tab in S2 File) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-43). Pathways uniquely identified in S. pneumoniae stimulated wild type alveolar macrophages are listed in rows 55-79. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 45-53) describes those functional categories. S15 Tab: Comparison of gene expression changes induced by S. pneumoniae in alveolar macrophages ex vivo. DEGs identified in S. pneumoniae stimulated vs unstimulated alveolar macrophages of either HRB-Mertk-/- (S9 Tab in S2 File) or wild type (S10 Tab in S2 File) mice were compared by finding the ratio of observed fold changes. The table list (A) DEGs originally identified in both genotypes (rows 4-78), (B) DEGs only identified in wild type mice (rows 84-272) or (C) DEGs only identified in HRB-Mertk-/- mice (rows 280-358) with a difference in expression >  2-fold (indicated by bold font). S16 Tab: Differentially expressed genes identified in naïve lung tissue of HRB-Mertk-/- vs wild type mice. Comparison of HRB-Mertk-/- vs wild type naïve left lung tissue. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. Asterisks indicate those DEGs similarly identified in Mertk-/- alveolar macrophages. S17 Tab: Differentially expressed genes identified in pneumonic lung tissue of HRB-Mertk-/- vs wild type mice. Comparison of HRB-Mertk-/- vs wild type pneumonic left lung tissue. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. S18 Tab: Gene ontology terms and Reactome pathways identified by functional enrichment analysis of pneumonic, HRB-Mertk-/- vs wild type left lung tissue. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in pneumonic, HRB-Mertk-/- vs wild type left lung tissue. The table list (A) gene ontology terms and (B) Reactome pathways enriched in HRB-Mertk-/- tissue (adjPval <  0.05) and are organized by normalized enrichment scores (NES). S19 Tab: Gene ontology terms identified by gene list over-representation analysis of DEGs in each k-means cluster comparing HRB-Mertk-/- vs wild type left lung tissue. k-means clustering analysis was performed on DEGs that changed>  ± 1.5-fold in HRB-Mertk-/- lung tissue. The analysis resulted in 6 clusters. Gene list over-representation analysis using DEGs was performed within each cluster. The table lists the statistically significant gene ontology terms enriched in (A) cluster 2 (rows 7-9) and (B) cluster 4 (rows 15-51). No GO terms were identified in clusters 1, 3, 5 or 6. GO pathways are organized by adjusted p value (padj). The number of DEGs (overlap) and their gene symbols (overlap genes) which were associated with each GO pathway are listed. (C) The DEGs used to perform k-means analysis and the clusters which they are associated with are listed (Column A, rows 56-487). S20 Tab: Differentially expressed genes identified in HRB-Mertk-/-, pneumonic vs naïve left lung tissue. Comparison of pneumonic vs naïve, left lung tissue isolated from HRB-Mertk-/- mice. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. S21 Tab: Differentially expressed genes identified in wild type, pneumonic vs naïve left lung tissue. Comparison of pneumonic vs naïve, left lung tissue isolated from wild type mice. The table list those DEGs that changed>  ± 1.5-fold and are organized by fold change. S22 Tab: Gene ontology terms identified by functional enrichment analysis of HRB-Mertk-/-, pneumonic vs naïve left lung tissue. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in pneumonic vs naïve HRB-Mertk-/- lung tissue. The table list those gene ontology terms enriched in pneumonic HRB-Mertk-/- lung tissue (adjPval <  0.05). Pathways similarly identified in pneumonic vs naïve, wild type lung tissue (S23 Tab in S2 File) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-704). Pathways uniquely identified in pneumonic HRB-Mertk-/- lung tissue are listed in rows 716-859. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 706-714) describes those functional categories. S23 Tab: Gene ontology terms identified by functional enrichment analysis of wild type, pneumonic vs naïve left lung tissue. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in pneumonic vs naïve wild type lung tissue. The table list those gene ontology terms enriched in pneumonic wild type lung tissue (adjPval <  0.05). Pathways similarly identified in pneumonic vs naïve, wild type lung tissue (S22 Tab in S2 File) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-704). Pathways uniquely identified in pneumonic wild type lung tissue are listed in rows 716-823. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 706-714) describes those functional categories. S24 Tab: Reactome pathways identified by functional enrichment analysis of HRB-Mertk-/-, pneumonic vs naïve left lung tissue. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in pneumonic vs naïve HRB-Mertk-/- lung tissue. The table list those Reactome pathways enriched in pneumonic HRB-Mertk-/- lung tissue (adjPval <  0.05). Pathways similarly identified in pneumonic vs naïve, wild type lung tissue (Supplemental Table 25) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-175). Pathways uniquely identified in pneumonic HRB-Mertk-/- lung tissue are listed in rows 187-219. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 177-185) describes those functional categories. S25 Tab: Reactome pathways identified by functional enrichment analysis of wild type, pneumonic vs naïve left lung tissue. Gene set enrichment analysis was performed using all expressed genes ranked by logFC in pneumonic vs naïve wild type lung tissue. The table list those Reactome pathways enriched in pneumonic wild type lung tissue (adjPval <  0.05). Pathways similarly identified in pneumonic vs naïve, HRB-Mertk-/- lung tissue (Supplemental Table 24) are highlighted in light yellow and are listed at the top of the table organized by normalized enrichment score (NES, rows 3-175). Pathways uniquely identified in pneumonic wild type lung tissue are listed in rows 187-221. Those pathways were manually grouped into functional categories and are organized first by category and second by normalized enrichment score (NES). The key provided (rows 177-185) describes those functional categories. S26 Tab: Comparison of gene expression changes induced by S. pneumoniae in left lung tissue. DEGs identified in pneumonic vs naïve lung tissue of either HRB-Mertk-/- (S21 Tab in S2 File) or wild type (S20 Tab in S2 File) mice were compared by finding the ratio of observed fold changes. The table list (A) DEGs identified in both genotypes (rows 4-71), (B) DEGs only identified in wild type mice (rows 74-91) or (C) DEGs only identified in HRB-Mertk-/- mice (rows 98-116) with a difference in expression >  2-fold (indicated by bold font). S27 Tab: Genes known to be located within the 129P2 insertion region on chromosome 2 and DEGs identified in naïve alveolar macrophages or lung tissue of HRB-Mertk-/- vs. wild type mice. (A) Genes located within the 129P2 DNA insert of chromosome 2. Listed in order of chromStart. DEGs identified in (B) naïve female alveolar macrophages, (C) male alveolar macrophages or (D) lung tissue of HRB-Mertk-/- vs. wild type mice. (E) Venn diagram comparing DEGs identified in alveolar macrophages and lung tissue.
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