title: GSM8966232: mouse liver cells; Mus musculus; RNA-Seq
library_construction_protocol: Intrahepatic CD45⁺ leukocytes and hepatocytes were isolated from the livers of two uninfected and two infected Alb Cre Ifnar1 Floxed mice (day 2 p.i.) following a previously described protocol (PMID: 33111119). Mice were euthanized using the isoflurane drop method. The inferior vena cava was cannulated, and the liver was sequentially perfused with 0.5M EDTA and collagenase solutions (Liberase, Sigma-Aldrich) using a peristaltic pump. The liver was then harvested, and viable hepatocytes and leukocytes were separated by density-based centrifugation with Percoll. Cells were filtered through a 70 µm strainer and collected into separate tubes for staining and sorting. Leukocytes were stained with APC anti-mouse CD45.2 (BioLegend). Dead cells were identified using SYTOX™ Blue Dead Cell Stain (ThermoFisher, #S34857) and Annexin-V (BioLegend, #640918). Each sample was tagged with TotalSeq-B anti-mouse hashtag antibodies 1-4 (BioLegend, #155831, #155833, #155835, #155837) to allow individual mouse identification. Leukocytes were sorted as CD45⁺ live cells, while hepatocytes were sorted as live cells using via a Sony SH800Z cell sorter. The final yield was approximately 4,000 CD45⁺ leukocytes and 1,000 hepatocytes per mouse. Post-sort single cell viability, assessed using propidium iodide/acridine orange staining on a Luna-FX7 cell counter, was around 85% for leukocytes and 56% for hepatocytes. All eight sorted samples (four leukocyte and four hepatocyte samples) were pooled into a single cell suspension, maintaining an 80:20 ratio of immune cells to hepatocytes. library construction was performed according to the manufacturer's instruction (Chromium Next GEM Single Cell 3' v3.1 kit, 10XGenomics)