library_construction_protocol: rats were euthanized by carbon dioxide inhalation at each time point. At 2 weeks post-op, cells were isolated from whole knee joint tissues, including synovium, ligament, infrapatellar fat pad, cartilage, and medial meniscus. The harvested tissues were minced, followed by 5 mg/ml collagenase I and IV in serum-free DMEM for 2.5 h at 37°. After enzymatic digestion, an equal volume of 10% FBS in DMEM was added to neutralize the enzymes. Suspended cells were transferred to a 100 µm strainer, centrifuged at 1,600 rpm, and rinsed 3 three times using PBS with 10% FBS. All cells from three animals per group were combined for scRNA-seq analysis. Library construction and scRNA-seq were performed on the 10XGenomics platform.