RNA-seq Analysis of Splenic CD11b+ Cells

CD11b⁺ splenocytes were isolated from wild-type recipient mice 11 weeks after BMT. For hypercholesteraemia experiments, BMT was conducted in Ldlr^−/− mice, four weeks after which a WTD was administered and sustained for seven weeks. Following WTD, mice were killed and CD11b⁺ splenocytes were collected and isolated into TRIzol reagent (Thermo Fisher Scientific). Aortic roots were also removed. RNA was isolated with RNeasy kits (Qiagen) and RNA-seq experiments were conducted as previously described^{37 (link)} on a NexSeq 500 (illumina). Genes were considered differentially expressed if they were significant at 5% false discovery rate (FDR) by DESeq2 and were at least twofold different in average reads per kilobase of transcript per million mapped reads (RPKM). Gene ontology analysis was conducted using the PANTHER database^{38 (link)}. Extended Data Fig. 1 displays RNA-seq data. All data have been deposited into a public repository.