FGF8-mediated gene regulation affects regional identity in human cerebral organoids

Single cell RNA sequencing Overall design: Human cortical organoids (day 69 of differentiation); 2 control batches (3 organoids each) and 2 FGF8-treated batches (3 organoids each). 17,400 cells per channel (corresponding to an estimated recovery of 10,000 cells per channel) were loaded onto a Chromium Single Cell 3' Chip (10x Genomics, PN 2000177). scRNA-seq libraries were prepared with the Chromium Single Cell 3' Library & Gel Bead Kit v.2 (10x Genomics, PN-120237). Libraries were sequenced using Illumina HiSeq 4000 system in Paired-End mode with 100 or 28 bases for read 1 and 100 bases for read 2, following Illumina's instructions. Image analysis and base calling were performed using RTA version 2.7.2 and Cell Ranger version 3.0.2.