CGD MoMacs fail to mature into resolving macrophages. Next-generation RNA-sequencing was performed on MoMacs isolated from WT or CGD mice at 6, 18, and 72 hours post–zymosan injection (post Zym), sorted according to Ly6C or MHCII expression (described in supplemental Figure 2). (A) Numbers of DEGs (twofold different with adjusted P values <.01) in each sample compared with the reference 6-hour WT sample. Symbol denotes MoMac phenotype, and color indicates genotype (WT [blue] or CGD [red]). (B-C) Analysis of genes that change expression between 18 and 72 hours after zymosan injection in the major population of WT MoMacs that do not similarly change expression in CGD samples (as described in the text). Gene expression changes were separated into transcripts either downregulated in WT (by less than −1.5 log₂FC) (B) or upregulated (by >1.5 log₂FC) (C). Adjusted P values for differential expression in this analysis were <.05. Heat maps show triplicate samples for the major population at each time point in either WT (blue) or CGD (red). Rows are minimum (Min)–maximum (Max) scaled to highlight samples with the maximum expression of each gene and ranked from top to bottom by differential expression between WT and CGD samples at 72 hours. (D) Gene Ontology overrepresentation tests were performed on genes identified as downregulated in WT from panel B (top) or upregulated in WT from panel C (bottom). Graphs show the top 10 enriched Biological Processes by number of genes per annotation.