Tissue architecture influences brain organoid identity and developmental trajectory
Tissue architecture influences brain organoid identity and developmental trajectory
Day55 brain organoids from hES H9 cell line were snap frozen and processed for single nuclei isolation. Single nuclei isolation protocol was adapted from “Frankestein protocol” (Hu et al., 2017; Habib et al., 2016; Habib et al., 2017; Lake et al., 2016)  and Denisenko et al., 2020. Tissue homogenate was FACS sorted to enrich for DAPI positive nuclei. Nuclei were further processed according to 10X manufacturing instructions\". Control (CTRL) organoids were generated according to the commercial kit (STEMdiff™ Cerebral Organoid Kit, StemCell Technologies 08570). Nucleic acid fragments were isolated and size-selected using Dynabead-based magnetic purification following 10x genomics library preparation protocol according to manufacturer's instructions. Single-nuclear RNA-seq libraries were generated using the 10X Genomics Chromium system (version 3 chemistry).