title: GSM6303895: single-cell RNA seq data of organoids cocultured with microglia; Homo sapiens; RNA-Seq
library_construction_protocol: We developed a 3D coculture of microglia in organoids. For this, we added microglia to the culture medium of preformed cerebral organoids that had been differentiated for 30 days according to the original Lancaster protocol. Following another 30 days of coculture, organoids were harvested. Immunohistochemistry demonstrated the presence of ramified IBA1+ cells in both superficial and deeper layers of the organoid, demonstrating survival and migration of microglia within the preformed organoid . We next performed single cell RNA sequencing by pooling and dissociating organoids to single cells and FACS-sorting for 3' microfluidics-based scRNA-seq (Chromium 10x). Three groups were compared: (i) microglia-like cells in vitro (2436 cells, 4204 median genes per cell) (ii) cerebral organoids (6642 cells, 3720 median genes per cell), and (iii) cerebral organoids with microglia (5873 cells, 4204 median genes per cell). The samples were loaded onto the 10x Genomics Chromium Single Cell Controller with the Chromium Single Cell 3' Library and Gel Beads Kit v3. Library preparation was carried out according to the manufacturer's instruction using AMPure beads (Beckman Coulter). Sequencing was performed on an Illumina Nextseq 6000 with a 150-8-0-150 read setup.