Single cell RNA-seq post valproic acid exposure in human forebrain organoids

Human forebrain organoids (day 50) derived from U1M and U2F iPS cell lines were exposed with or without 1 mM valproic acid (VPA) for 72h. Organoids were then used for single cell RNA sequencing (scRNA-seq). Through data processing, ten major cell types including astrocyte, choroid plexus, endothelia, intermediate progenitor cells, medial ganglionic eminence, radial glia, immature neuron, excitatory and inhibitory neuron, and microglia-like cells were identified. We found that VPA affected gene expression in choroid plexus, excitatory neuron, immature neuron, and medial ganglionic eminence cells. The cell type-specific DEGs were enriched with mitotic nuclear division, multiple neuronal functions, and response to type I interferon and virus. Overall design: We generated human forebrain organoids from U1M and U2F iPS cell lines. On day 50, human forebrain organoids derived from both U1M and U2F were exposed with or without 1 mM VPA for 72h. Three organoids in each group were randomly pooled together to prepare single cell suspension using Accutase. 2x104 cells per sample were used for cell capture using the 10x Genomics system. The captured cells were then used for reverse-transcription and library constructions based on the standard Illumina protocols. The constructed libraries were then sequenced on Illumina NovaSeq 6000 (paired-end 150 bp). We then performed differential gene expression analysis to identify genes affected by VPA exposure in each cell type identified in the organoids.