characteristics.text: 2026-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: IIMCB
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS20599313
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14253:TREM2 fibrosis 1
characteristics.characteristic: Submitter Id
characteristics.text: 17
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: 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. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: TREM2 KO
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: 3
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: liver
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: TREM2 KO
characteristics.characteristic: strain
characteristics.text: TREM2 fibrosis 1
characteristics.characteristic: title