Fig. 4

Differential gene expression of bulk sorted SIRPα⁻ or SIRPα⁺ transgenic CD8⁺PD-1⁺ T cells. CD8⁺ T cells from naive Friend virus (FV)-specific Thy1.1⁺ CD8.TCR transgenic mice were transferred i.v. into Y10 mice chronically infected with FV. After 13–15 days, CD8⁺ cells were purified from the spleens of these recipients using anti-CD8 paramagnetic beads and the Miltenyi MACS systems. Cells were then stained with anti-Thy1.1; anti-CD8; anti-PD-1; and anti-SIRPα and sorted into CD8⁺Thy1.1⁺PD-1⁺SIRPα⁻ and CD8⁺Thy1.1⁺PD-1⁺SIRPα⁺ populations for analysis using a BD FACSAriaIIu. A heat map representation of the top 325 differentially expressed genes between the SIRPα⁻ and SIRPα⁺ transgenic CD8⁺PD-1⁺ T cells was generated using the Benjamini–Hochberg procedure to decrease the false discovery rate (FDR) using DESeq2 default settings (FDR ≤ 0.1). Selected differentially expressed genes are highlighted on the left. Heat map is color coded by row z-score as shown