Mus musculus
Protocols: Synovial cells were isolated followed by cell sorting through a 70-μm nozzle using the Fusion Q cell sorter. Prior to sorting, DAPI (4′,6-diamidino-2-phenylindole) (Thermo Fisher) was added to the cell suspension to exclude dead cells. Sorted populations included non-neutrophil immune cells (DAPI- CD45+ Ly6G-) and fibroblasts/endothelial cells (DAPI- CD45- CD31+ or Podoplanin+). Post-sort cell count showed that all sorted populations exhibited a viability exceeding 90%. Before loading cells sorted cells to the 10X platform, the immune cells were pooled with the sorted fibroblasts/endothelial cells. Gene expression (GEX) and multiplex (CMO) libraries were generated using the Chromium Single Cell 3' Reagent Kit V3.1 from 10X Genomics following the manufacturer's instructions. Each sample loaded onto a 10X Genomics cartridge consisted of up to 60,000 cells. Different litters or sexes were pooled before sorting using the 3' CellPlex Kit Set A, following the manufacturer's instructions (10X Genomics).  GEX and CMO libraries were purified using SPRIselect beads (Beckman Coulter). The libraries were quantified and assessed for size distribution on the Qubit 2.0 Fluorometer (Thermo Fisher) and the Agilent Bioanalyzer (Agilent Technologies) using the Qubit dsDNA HS assay Kit and the DNA HS Kit, respectively. Results were utilized to calculate the library molarity. Library preparation and quality control were conducted at the IRR Cell Sorting Facility.
ENA first public
2026-06-16
INSDC center name
Institute for Regeneration & Repair Centre for Reproductive Health University of Edinburgh, UK
INSDC status
public
Submitter Id
E-MTAB-17170:Sample RG20_GEX
age
1
broker name
ArrayExpress
cell type
macrophage, fibroblast, endothelial cell
collection date
not collected
common name
house mouse
genotype
Cdh5CreERT2+/-:Rosa26lsl-tdT+/-:Cx3cr1gfp+/-
geographic location (country and/or sea)
not collected
individual
Mixed_Litter
isolate
not applicable
organism part
synovial membrane
protocol
GEX
sample name
E-MTAB-17170:Sample RG20_GEX
scientific_name
Mus musculus
sex
Mix
strain
Cdh5CreERT2:Rosa26lsl-tdT:Cx3cr1gfp