Single-cell RNA sequencing of CD45+ immune cells across primary tumor, sentinel tumor-draining lymph node, and axillary lymph node in treatment-naive triple-negative breast cancer

Regional lymph node metastasis critically influences distant metastatic progression, anti-tumor immunity, and patient prognosis in triple-negative breast cancer (TNBC). In this study, fresh surgically resected specimens from treatment-naive TNBC patients were collected and CD45+ immune cells were isolated for single-cell RNA sequencing to characterize immune remodeling across matched primary tumors, sentinel tumor-draining lymph nodes (S-TDLNs), and secondary axillary lymph nodes (ALNs). The overall project integrated scRNA-seq with imaging mass cytometry, Visium and Xenium spatial transcriptomics, and multiplex immunofluorescence. This GEO submission contains processed scRNA-seq expression matrices and associated metadata only. Raw sequencing data have been deposited previously in in the Genome Sequence Archive (GSA) for human data, and the GSA ID is HRA010347.