Fig. 1

TBI increases the expression of genes associated with immune response, and decreases the expression of genes connected to ion transmembrane transport. RNA was isolated from the hippocampal and cortical tissues collected 14 days after injury from Abca1^+/− and Abca1^+/+ mice of both APOE isoforms and was then used to perform RNA-seq, N = 6–8 mice per group of both genders. a-d Scatter plots represent the RNA-seq results for differentially expressed genes. EdgeR analysis between sham and injured mice identified significant affected transcripts in (a) APOE3/Abca1^+/−, (b) APOE4/Abca1^+/−, (c) APOE3/Abca1^+/+ and (d) APOE4/Abca1^+/+ mice. Red denotes up-regulated, and blue denotes down-regulated genes, p < 0.05. e Heatmap of the top 100 upregulated and downregulated genes by TBI is shown. f A table shows the top annotated GO terms derived from the common, upregulated genes (total = 1215 genes). g A table shows the top annotated GO terms derived from the common, downregulated genes (total = 531 genes)