For deep RNA sequencing, libraries for three biological replicates of 4-week-old forebrain neurons derived from iPS cells of three individuals within the pedigree H (C3-1, D2-1 and D3-2) without astrocyte co-culture were prepared and sequenced on an Ion Proton Torrent. Libraries were prepared using the Ion Total RNA-Seq Kit v2 for Whole Transcriptome sequencing following the protocol provided by the manufacturer (Life Technologies, Carlsbad, CA). Briefly, poly (A)-enriched mRNA samples were fragmented, Ion Adaptors were hybridized, and cDNA generated through reverse transcription. Barcodes were added and the libraries were amplified for sequencing. From the poly(A)+ RNA-seq libraries, a total of 123 million reads were generated comprising between 9 and 34 million reads from each of the 9 samples (Supplementary Table 2a). Sequencing generated strand-specific singleend reads of variable length between 8–24 bp. Reads were mapped to the UCSC Human Reference Genome (hg19) using TopHat36 (v2.0.10) and Bowtie37 (v2.1.0). Resulting sequence alignment files were analysed using RSeQC package for quality control38. Reads covering gene coding regions were counted with BED Tools and count data were analysed for differential expression using edgeR39
