Single-cell RNA-seq Analysis of Plasmacytoid Dendritic Cells (pDCs) in Systemic Lupus Erythematosus (SLE)

Overview: This dataset contains processed single-cell RNA-sequencing (scRNA-seq) data derived from human plasmacytoid dendritic cells (pDCs) isolated from patients with Systemic Lupus Erythematosus (SLE) and healthy controls. The data was used to characterize the SOX4-CXCR4 regulon and its role in SLE pathogenesis. Dataset Contents: SLE_pDC_Cleaned_For_pySCENIC.h5ad: The pre-processed AnnData object containing normalized gene expression matrices, filtered for high-quality female pDC populations. SLE_pDC_Integrated.h5ad: The batch-corrected dataset (using Harmony) used for UMAP visualization and downstream integration analysis. SLE_pDC_pySCENIC_Complete.h5ad: The final AnnData object containing integrated regulon activity scores (AUC) calculated via pySCENIC. Methodology: Data was processed using the scanpy workflow. Network inference was performed using pySCENIC (GRNBoost2). Batch effect correction was performed using harmonypy to integrate data from 242 donors. Usage: This data is provided to ensure reproducibility of the findings reported in the manuscript. For analysis scripts, please refer to the associated anonymous GitHub repository: https://anonymous.4open.science/r/SLE_pDC_SOX4_Analysis-2038 Terms of Use: This data is made available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Please cite this dataset if used in your research.