biostudies-arrayexpressAleksandra KolodziejczykMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14253The goal of this study is to understand the effect of fibrosis on the cell frequencies and gene expression in liver in Trem2KO mice. To achieve that we performed single cell sequencing of liver cells from whole-body Trem2 KO mice treated with thioacetamide to induce liver fibrosis.biostudies-arrayexpressSample Collection - Liver cells were isolated using a modified protocol of Mederacke et al.22 In brief, using a peristaltic pump we performed retrograde liver perfusion into the inferior vena cava with three solutions: (1) EGTA (8 g/l NaCl, 0.4 g/l KCl, 88 mg/l NaH2PO4∙H2O, 120 mg/l Na2HPO4∙H2O, 2.38 g/l HEPES, 0.35 g/l NaHCO3, 0.19 g/l EGTA, 0.9 g/l glucose) for 2 min; (2) pronase (0.4 mg/ml Protease from Streptomyces griseus in EBS buffer: 8 g/l NaCl, 0.4 g/l KCl, 88 mg/l NaH2PO4∙H2O, 120 mg/l Na2HPO4∙H2O, 2.38 g/l HEPES, 0.35 g/l NaHCO3, 0.42 g/l CaCl2) for 5 min; and (3) collagenase D (0.1U/ml collagenase D in EBS buffer) for 7 min. The liver was then dissected, placed in cold EBS solution and shaken vigorously with forceps to allow separation of single cells. The solution was filtered through 100-μm mesh and hepatocytes were depleted by centrifugation at 30g for 5 min. Cells were then collected by centrifugation at 580g and resuspended in cold Ca/Mg-free PBS. To enrich for stellate cells, we sorted cells with retinoid fluorescence in the channel excitation 405, emission 450/40 using a BD FACSAria III. We then mixed stellate and unsorted cells in 1:1 ratio, spun them down, resuspended them in Ca/Mg-free PBS with 0.04% BSA and counted them using a Neubauer chamber, before proceeding to single-cell RNA-seq.Library Construction - according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User GuideNucleic Acid Extraction - according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User GuideSequencing - according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User GuideOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Data was analysed using Cell Ranger pipeline v6.0.0 and mapped to mouse genomeData Transformation - Data was analysed using Cell Ranger pipeline v6.0.0 and mapped to mouse genomeUnknownTranscriptomicsGenomicsProteomics10x Genomics ChromiumNextSeq 550manualRNA-seq of coding RNA from single cellsMus musculusAleksandra Kolodziejczykfalsesingle cell RNA sequencing of liver cells in TREM2 KO miceThe goal of this study is to understand the effect of fibrosis on the cell frequencies and gene expression in liver in Trem2KO mice. To achieve that we performed single cell sequencing of liver cells from whole-body Trem2 KO mice treated with thioacetamide to induce liver fibrosis.2026-01-01T00:00:00Z2026-01-01T02:02:02.011Z2024-07-19T15:47:04.463ZE-MTAB-14253ERP162167EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184