EBs were fed every other day for 6 days then transferred to low adhesion 24-well plates (Corning) in neural induction media containing DMEM/F12, 1:100 N2 supplement (Invitrogen), Glutamax (Invitrogen), MEM-NEAA, and 1ug/ml Heparin50 (link) (Sigma). These began forming neuroepithelial tissues, which were fed every other day for 5 days. On Day 11 of the protocol, tissues were transferred to droplets of Matrigel (BD Biosciences) by pipetting into cold Matrigel on a sheet of Parafilm with small 3mm dimples. These droplets were allowed to gel at 37C and were subsequently removed from the Parafilm and grown in differentiation media containing a 1:1 mixture of DMEM/F12 and Neurobasal containing 1:200 N2 supplement (Invitrogen), 1:100 B27 supplement without vitamin A (Invitrogen), 3.5ul/L 2-mercaptoethanol, 1:4000 insulin (Sigma), 1:100 Glutamax (Invitrogen), 1:200 MEM-NEAA.
After 4 days of stationary growth, the tissue droplets were transferred to a spinning bioreactor containing differentiation media as above except B27 supplement with vitamin A (Invitrogen) was used. Since retinoic acid has been shown to be important for neuronal differentiation in vivo52 (link), we included it in the final media used to differentiate the cerebral organoids.