Staining and acquisition

Cells were prepared as above. Samples stained with the T cell-focused panel were first stained with custom HBV-specific tetramers developed by the National Institutes of Health (NIH) Tetramer Core Facility at Emory University. Cells were stained first with MHC Class II Tetramer for 1 hour at 37°C protected from light. Next, these cells were then stained with MHC Class I Tetramer for 1 hour at 4°C protected from light. For both panels, cells were then stained with Live/Dead Fixable Blue (Thermo Fisher Scientific) according to the manufacturer’s instructions. Next, surface markers on cells were stained according to standard protocols with anti-mouse antibodies detailed in Supplemental Table 2 (Myeloid-focused Panel) or Supplemental Table 3 (T cell-focused Panel). Finally, cells were fixed and permeabilized using FoxP3/Transcription Factor Staining Buffer Set (Thermo Fisher Scientific, cat. 00-5523-00) and stained with anti-mouse antibodies targeting intracellular markers according to standard protocols.