Systematic Comparison of Droplet‐Based and Microwell‐Based Platforms for Comprehensive Single‐Cell Transcriptomic Analysis in Clinical Samples

Single-cell RNA sequencing (scRNA-seq) is widely utilized in tumor research. However, platform-specific technical biases may impact data interpretation. This study compared the performance of droplet- and microwell-based scRNA-seq platforms in the analysis of clinical samples. Despite the similarities after batch effect correction, significant differences were observed in multiple aspects, including mRNA preference, cell type restoration, and gene expression patterns. The droplet-based platform captured a higher proportion of immune cells, whereas the microwell-based platform provided a more accurate immune cell representation. Differential gene expression, pseudotime, and cell-cell communication analyses further revealed platform-dependent variations across multiple aspects. Overall, this study provides valuable insights into platform selection and optimization for cross-platform data integration in single-cell transcriptomics.