This repository contains the raw single-cell gene-expression matrices and analysis code associated with the study “Gene–environment interactions converge on lysosomal dysfunction in Alzheimer's disease cerebral organoids.” The scRNA-seq dataset was generated from day-60 wild-type human cerebral organoids and was used to characterize the baseline cellular composition of the organoid model. After quality control, ambient RNA correction and doublet removal, 7,249 cells were retained for downstream analysis. The annotated cell populations include radial glia, neural progenitor cells, intermediate progenitor cells, immature neurons, inhibitory neurons, SLC17A6-positive excitatory neurons, SLC17A7-positive excitatory neurons, astrocytes and choroid plexus-like cells. The deposited files include raw cell-gene expression matrices generated from the sequencing data and R scripts used for quality control, ambient RNA correction, decontamination, doublet removal, normalization, clustering, UMAP visualization and cell-type composition analysis. The analysis workflow uses Seurat together with SoupX, DecontX and scDblFinder. These data and scripts support the scRNA-seq analyses shown in Fig. 1 and Fig. S2 of the manuscript and are provided to enable inspection, reproduction and reuse of the day-60 cerebral organoid cell-type annotation analysis.