Skip to main content
. Author manuscript; available in PMC: 2018 Jun 11.
Published in final edited form as: Nat Genet. 2017 Dec 11;50(1):54–61. doi: 10.1038/s41588-017-0005-8

Figure 3. Gene expression variability in IPSDSNs is influenced by differentiation conditions.

Figure 3

(a) Density plot of the coefficient of variation of genes across samples, separately for each GTEx tissue, IPSDSN samples (n=106, P2 protocol only), iPSC (n=239), and DRG (n=28). (b) Violin plot showing, for each gene, the estimated fraction of total expression variability across samples due to differentiation batch, donor genetics or iPSC reprogramming, culture conditions (“wasFeeder”: feeder-dependent vs. E8 medium), and gender. (c) Differentially expressed genes (FDR 1%, blue and red points) between iPSC samples grown on feeders (n=68) vs. E8 medium (n=171). (d) Differentially expressed genes (FDR 1%) between IPSDSNs from feeder- (n=27) and E8-iPSCs (n=79). Neuronal differentiation genes, such as RET and L1CAM, are more highly expressed in samples from E8-iPSCs. (e) Left boxplot: global gene expression differences between feeder- and E8-iPSCs are captured in PC1. Right two boxplots: selected differentially expressed genes. (f) Left boxplot: estimated neural fraction of samples differs in IPSDSNs derived from feeder- and E8-iPSCs. Right two boxplots: selected differentially expressed genes. Boxplots show the median, 25th and 75th percentiles, with whiskers extending 1.5 times the interquartile range.

HHS Vulnerability Disclosure