Fig. 3: RNAseq analysis reveals a role for post-resolution macrophage populations in T cell migration/maturation.

WT C57BL6/J mice were administered intranasal S. pneumoniae with lungs digested and macrophage populations including (A) double negative interstitial macrophage, (B) LYVE-1^-/MHC-II⁺ interstitial macrophages, (C) LYVE-1⁺/MHC-II^- interstitial macrophages as well as (D) alveolar macrophages sorted by FACS and subject to analysis by RNAseq followed by bioinformatic analysis using edgeR in RStudio as illustrated (n = 5 mice/group). D qPCR validation (n = 3 mice/group) was used in a separate independent experiment to confirm upregulation of Inhba and Ptgs2 in naïve versus day 14 alveolar macrophages. Students unpaired t-test was used to compare the means of two groups. A p value of <0.05 was taken as the threshold of significance with graphical representation as; p < 0.05 = *, p < 0.01 = ** and p < 0.001 = *** and presented as mean ± SEM. As alveolar macrophages showed the greatest changes post-resolution compared to the naive state these cells were further analysed by using (E) PANTHER to identify GoTerms from upregulated genes at day 14 compared to naïve, (F, G) normalised read counts of five replicates from naïve alveolar macrophages compared to day 14, (H) EdgeR results showing differential gene expression as logFC and p value for genes relating to migration, matrix remodelling, regulation of phenotype and interferon signalling.