chromium microfluidic chip  (10X Genomics)

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Multitechnological integration advances musculoskeletal regeneration: synergistic progress of organoids, 3D/4D bioprinting, single-cell omics and artificial intelligence

doi: 10.3389/fbioe.2026.1824644

Figure Lengend Snippet: Workflow of single-cell omics in musculoskeletal regeneration research. Six core steps are depicted: (1) Tissue dissociation to obtain high-viability single-cell suspension; (2) Single-cell capture using microfluidic platforms; (3) Library preparation for scRNA-seq/scATAC-seq; (4) High-throughput sequencing with controlled reads per cell; (5) Data preprocessing including quality control and normalization; (6) Bioinformatics analysis for cell clustering, trajectory, and gene regulatory network construction.

Article Snippet: The methodological workflow of musculoskeletal single-cell omics research includes six core steps: (1) Tissue dissociation: enzymatic digestion (collagenase, trypsin) of fresh musculoskeletal tissue (bone, cartilage, tendon, muscle) to obtain single-cell suspensions with a viability >80% (2) Single-cell capture: using microfluidic chips (e.g., 10x Genomics Chromium); or droplet-based systems to capture individual cells; (3) Library preparation: reverse transcription of single-cell RNA to cDNA, and amplification for scRNA-seq, or chromatin fragmentation and sequencing for scATAC-seq; (4) Sequencing: high-throughput sequencing with a sequencing depth of 50,000–100,000 reads per cell for scRNA-seq, and 20,000–50,000 reads per cell for scATAC-seq; (5) Data preprocessing: quality control (removal of low-quality cells and doublets), normalization and dimensionality reduction (PCA, t-SNE, UMAP); (6) Bioinformatics analysis: cell clustering, cell type annotation, differential gene expression analysis, cell trajectory analysis and gene regulatory network (GRN) construction ( ; ; ).

Techniques: Single Cell, Suspension, Next-Generation Sequencing, Control