Preparation of cDNA libraries (TruSeq Kit, Illumina) and sequencing (HiSeq 2500, Illumina) were performed by RUCDR Infinite Biologics® (Piscataway, NJ). Data were aligned with human genome using TopHat55 and analyzed with Cuffdiff and R/BioConductor using the cummeRbund package5556. Sequencing data can be found in NIH repositories (SRA accession number SRP040275; GEO accession number GSE56398). H1 hESC-derived NSC data for days 0 and 5 are part of GEO series GSE5678536. Datasets for DA neuron cultures were from the following SRA accession numbers: SRR1030497, SRR1030496, SRR1030493, and SRR103049235.
