Pair-ended RNA-seq data was generated using the Illumina HiSeq 2500 platform for hiPSC-astrocytes (four lines), neurons (six lines), and NPCs (eight lines) (Table S2), as well as for two primary astrocyte samples. The pair-ended sequencing reads were aligned to human hg19 genome using Star Aligner (version 2.5.0b). Following read alignment, featureCounts (Liao et al., 2014) was used to quantify the gene expression at the gene level based on Ensembl gene model GRCh37.70. Gene expression data preprocessing and downstream analyses, including differential gene expression and functional enrichment, are detailed in Supplemental Experimental Procedures.
