Supplementary Figure 3: Transcriptome analysis of BMDMs treated with HDL.

a-c,e,f, Transcriptome data are derived from BMDMs pre-treated for 6 h with HDL (2 mg/ml) then stimulated for 4 h with CpG (100 nM). a, Principal component analysis of all genes demonstrating sample relationships and group associations of individual samples. b, Hierarchical clustering of the 1000 most variable genes within the dataset. c Visualisation of genes (fold change values) involved in the cholesterol biosynthesis pathway from HDL treated BMDMs. d, Immortalised-BMDMs were treated with 2 mg/ml HDL for indicated times and cholesterol precursors were measured by mass spectrometry. e, Network visualization of Gene Ontology Enrichment Analysis (GOEA) based on transcripts reduced by CpG and counter-regulated by HDL (red nodes: GO-terms, red edges: GO-term relations) or induced by CpG and counter-regulated by HDL (blue edges and nodes). f, Workflow scheme of transcription factor prediction modelling. a-c,e,f, At least three biological replicates per condition were generated. d, Representative graphs of two individual experiments are presented (mean ±S.D.).