Macrophage subpopulation-specific impairments in expression of MHC Class II. Genome-wide transcriptional analysis was performed by microarray of RNA extracted from spleen tissue of mice recovered 1, 2, or 5 days after middle cerebral artery occlusion (MCAO) or sham surgery. The fold-change of macrophage-associated gene expression levels was analyzed in relation to expression measured in spleens from sham-operated animals (A) Analysis of the H2 genes which encode mouse MHC class II show downregulation of expression of all H2 genes 1–5 days after MCAO in comparison to sham-operated animals (sham n = 2, 1 day and 2 days n = 3, 5 days n = 4). (B) MHC Class II (green) immunolabelling along with labeling for marginal zone macrophages (MZM) (red, MARCO; top panel), both tissue resident and monocyte-derived RPM (blue, F4/80 top panel), tingible body macrophages (red, MOMA-2 within white pulp; middle panel), classical dendritic cells (blue, CD11c middle panel), marginal zone metallophillic macrophages (red, MOMA-1; bottom panel) or monocyte-derived RPM only (blue, CD11b; bottom panel) to determine co-localization of MHC Class II on splenic macrophage subsets. Image analysis determined the percentage of (C) MOMA-2, (D) CD11c, (E) MOMA-1, (F) MARCO, (G) F4/80, and (H) CD11b immunolabelling that co-localized with MHC class II immunolabelling 1–7 days after MCAO in comparison to sham-operated or naïve controls (naïve n = 4, sham n = 4, 1 day n = 4, 2 days n = 9, 5 days n = 5, 7 days n = 7). Scale bars 100 µm. Data show mean ± SD *P < 0.05; ***P < 0.005; (C–H) one-way analysis of variance with Bonferonni correction.