Fig. 3: Transcriptional downregulation of lipid metabolic pathways in CD1d-KO cells.

a pMacs isolated from WT or CD1d-KO mice were subjected to RNAseq analyses (n = 4). Top left, volcano plot including differentially expressed genes (black). A fold change cut-off of 1.5 and adjusted p-value cut off of 0.01 were applied. Top right, functional enrichment analysis of genes significantly changed in WT vs. CD1d-KO pMacs. The GO terms are shown ranked by p-values. Enrichment and p-values (from a Fisher’s exact test with Bonferroni correction) were calculated with PANTHER tools. Bottom left, heat map for selected transcripts significantly changed in WT vs. CD1d-KO pMacs. Bottom right, representative image of the cholesterol biosynthesis pathway, showing metabolites and enzymes responsible for the individual synthetic step. Enzymes encoded by genes significantly downregulated in CD1d-KO pMacs are shown in blue. b–f qPCR analyses showing relative expression of the depicted genes in WT (blue) and CD1d-KO (red) pMacs, pMacs sort purified from 50:50 WT:CD1d-KO bone-marrow chimeras and BMDCs as indicated (n = 4–11). Bars represent mean +/− SEM; *p < 0.05; **p < 0.01; ***p < 0.001, one-sample t-test. Values for n represent biologically independent samples (as shown by the number of data points in each graph). n = cells isolated from individual mice. Source data are provided as a Source Data file.