NextSeq 550 paired end sequencing; RNA-seq of INPP5E mutant cortical organoids against control organoids
Organoids were collected in 1.5ml Eppendorff tubes and washed three times in 1xPBS. The supernatant of the final wash was discarded and organoids were shock frozen on dry ice and stored at -80C.  Total RNA was extracted using the QIAGEN RNeasy Plus Micro kit as per manufacturer's instructions. RNA was eluated in 14 μl of RNAse free water.  Libraries were prepared from 250ng of each total-RNA sample using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the provided protocol