library_construction_protocol: For bisulphite sequencing of iPSCs and neurons, genomic DNA was extracted from cultured cells with the Qiagen DNeasy Blood and Tissue kit (Qiagen, 69504) or the Zymo QuickDNA Miniprep kit (Zymo D3024). gDNA was stored at -80C. 250ng of gDNA were input into the bisulphite conversion reaction. For bisulphite conversion and purification, we used the Zymo EZ DNA Methylation Gold kit as instructed (Zymo, D5005). 2uL of bisulphite-converted gDNA was used as input for PCR as described above, with an annealing temperature of 57C. PCR1 reactions were then cleaned with Ampure XP beads (Beckman, A63881) at a ratio of 1.8x. 1/10th of PCR1 was used as input for PCR2 with Q5 polymerase. PCR2 added i5 and i7 barcodes and P5 and P7 overhangs for dual-index Illumina short read sequencing. PCR2 products were purified with Ampure XP beads. Products were visualized via electrophoresis on an Agilent TapeStation 4200 and quantified with Qubit dsDNA HS assay kit (Invitrogen, Q32851) on a Qubit fluorometer (Invitrogen). Libraries were pooled and sequenced on an Illumina Miseq instrument with a Miseq v3 600 cycle kit (Illumina, MS-102-3003) with read lengths of 250x250.