Micro-region transcriptomics profiling of cerebral organoids using a capillary-based microdissection system

Investigating the transcriptome while preserving cellular spatial information facilitates a comprehensive understanding of cellular fates in multicellular organisms. However, the precise and flexible isolation of micro-regions of interest (mROIs) for profiling spatial transcriptomics (ST) remains a challenge. We established a capillary-based tissue microdissection system (CMS), which enables the high-efficiency acquisition of mROIs from cultured cerebral organoids for mRNA sequencing (CMS-seq). Subsequently, neural progenitor cells (NPCs), intermediate progenitors (IPs), mature neurons, and astrocytes were annotated in the cerebral organoids at the stages of days 20 and 60, respectively. Furthermore, astrocytes in the samples from day 20 were found to exhibit a higher tendency to express the <i>SPARC</i> gene whereas those from day 60 showed a stronger tendency to express the <i>NTRK2</i> gene. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes indicated a higher degree of neural development at the stage of day 60. Finally, a spatial annotation map of cell types of the mROIs was constructed, enabling rapid identification of the cellular composition in each mROI. Therefore, we established an efficient method for ST analysis in cerebral organoids and further exploration of the spatial developmental trajectory.