Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset

Human induced pluripotent stem cell-derived neural progenitor cells (NPCs) provide a controlled in-vitro model for studying early stages of neuronal differentiation. Here, we present a multimodal single-cell dataset generated from NPCs differentiated over four time points (days 0, 7, 13 and 20) under baseline conditions and following exposure to amyloid-β (Aβ) 1-42 peptide. The dataset comprises paired single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) profiles, enabling joint characterization of transcriptional and chromatin accessibility dynamics during differentiation. Following stringent quality control, we analyzed 42575 and 30192 high-quality cells for RNA and ATAC respectively, providing an in-depth characterization of cell composition, molecular signaling pathways, functional properties, and gene regulatory network annotations. To facilitate reuse and benchmarking, transcriptional signatures derived from this dataset were additionally compared with a publicly available human hippocampal bulk RNA-seq dataset. This resource provides a reference multimodal dataset for human NPC-derived neuronal differentiation and supports a broad range of single-cell, multimodal integration, and regulatory network analyses.