Immune cells from liver after MCMV infection were FACS sorted prior to capture.  For Multiome, nuclei were isolated by lysing cells for 3 min in 100 µl of freshly made lysis buffer (10 mM Tris-HCl-pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% Nonidet P-40 Substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, and 1000 U/ml of RNase inhibitor). Nuclei were washed twice with freshly made Wash Buffer (10 mM Tris-HCl-pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1% BSA, 1 mM DTT, and 1 U/µl RNase inhibitor) and resuspended in 1x Nuclei Buffer (10x Genomics) for Tn5 incubation. For CITEseq, cells were stained with TotalSeq Hashtag antibodies and TotalSeq ADT antibodies prior to capture. We used Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics) to generate scRNA-Seq and scATAC-Seq libraries according to the manufacturer's protocol. We used Chromium Next GEM Single Cell 5' HT v2 Kit and 5' Feature Barcode kit (10x Genomics) to generate CITE-seq libraries according to the manufacturer's protocol.