RNA-seq samples were clustered based on all expressed transcripts (average FPKM > 1, n = 17,669, Additional file 3: Figure S1A) or a list of selective neural stem cell and differentiating neuronal markers obtained from R&D Systems (http://www.rndsystems.com/molecule_group.aspx?g=824&r=7) (n =55; Additional file 3: Figure S1B). We performed UPGMA (unweighted pair group method with arithmetic mean) clustering of samples from transcriptomic profile similarities based on the Pearson correlation coefficients. The analysis showed that our samples could be separated into two clusters; the cluster membership did not change whether all transcripts or only the neural marker genes were used for clustering. The first cluster (left on the heatmaps in Additional file 3: Figure S1B) exhibited higher expression of neuronal markers (e.g., TUBB3 and MAP2), while the second (right on the heatmaps in Additional file 3: Figure S1B) showed greater expression for neural stem cell and neural progenitor markers (e.g., VIM, SMAD2 and NOTCH2). These suggest that variation in the degrees of neuron differentiation and maturation existed in our samples and needs to be accounted for in the differential expression analysis. Note that
