Supplementary Figure 5: Transcriptome analysis of WT vs Atf3-deficient BMDMs.

Microarray analysis of WT or Atf3-deficient BMDMs pre-treated with 2 mg/ml HDL for 6 h and subsequently stimulated with CpG (100 nM) or P3C (50 ng/ml) for 4 h. a, Visualisation of transcripts induced or repressed by P3C in WT, counter regulated by HDL pre-treatment, and no longer modified in Atf3-deficient BMDMs. b, Venn diagrams show the overlap between CpG and P3C conditions from genes identified using the model described. c Network visualization of GOEA: GO-terms (nodes) and their relation (edges) based on ATF3-independent genes are shown in blue, and those based on ATF3-dependent genes are shown in red. d, Visualisation in fold change of genes involved in the cholesterol biosynthesis pathway from HDL treated WT or Atf3-deficient BMDMs. e, 27 of the 130 transcripts altered by CpG, counter-regulated by HDL and no longer modified in Atf3-deficient BMDMs are direct ATF3-target genes. Network visualization of GOEA based on transcripts reduced by CpG, counter-regulated by HDL and no longer modified in Atf3-deficient BMDMs showing ATF3 binding by ChIP-Seq (red nodes: GO-terms, red edges: GO-term relations) or induced by CpG and counter-regulated by HDL and no longer modified in Atf3-deficient BMDMs showing ATF3 binding (blue edges and nodes). a-e, At least three biological replicates per condition were generated and analysed.