scRNA-seq was performed on eight untreated and six METH-treated organoids. Organoids were manually dissociated into single-cell suspension using the Milteny Biotec Neural Tissue Dissociation Kit (P) (Milteny Biotec, 130–092–628) following manufacturer's instructions. Briefly, organoids were washed with PBS and cut into small pieces using a scalpel. Tissues were resuspended in warmed enzyme mix 1 containing papain and rotated for 15 min at 37 °C. Enzyme mix 2 was added and tissues were mechanically dissociated using a wide-tipped pipet. Cell suspensions were passed through a 40 μm cell strainer and centrifuged to pellet. Cell concentrations and viability were assessed by trypan blue staining. scRNA-seq libraries were generated using the 10x Genomics Chromium Single-cell 3′ Library & Gel Bead Kit V2 (10x Genomics, PN-120237) at the UCSD Institute for Genomic Medicine Genomic Center. Libraries were generated from organoid single-cell suspensions following manufacturer's protocol.