Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [TRAP-seq]

Atherosclerotic coronary artery disease (CAD) development encompasses changes in immune cell activation across different tissues, including vascular and metabolic tissues. However, the specific disease-associated transcriptional changes occurring within each of the tissue cell types remain incompletely characterized. Here, we combine an atherosclerosis mouse model with a mouse strain designed for translating ribosome affinity purification followed by RNA sequencing (TRAP-Seq). The mice express a fusion protein of EGFP and ribosomal protein L10a (EGFP-L10a) under the control of the macrophage-specific Csf1r (Cfms) promoter. Using EGFP as an affinity tag, this enables the enrichment of macrophage-specific ribosome-associated RNA from whole tissue lysates. Here, we profile the macrophage-enriched RNA fraction from aorta, liver and adipose tissue. A disease stage course of atherosclerosis in mouse was established by varying genotype (wild type and proatherogenic LDLR-/- ApoB100/100) and diet (0, 1 or 3 months of high-fat diet) in mice expressing EGFP-tagged ribosomal protein L10a (EGFP-L10a) under the control of a macrophage-specific promoter. Using the EGFP-L10a transgene, TRAP-Seq was performed from aorta, liver and perigonadal adipose tissue (epididymal in male and periovarial in female) to sequence macrophage-enriched RNA.