Fig. 1
From: Codon usage optimization in pluripotent embryonic stem cells
Profiling mRNA expression and translation in self-renewing and differentiating hESCs. a Treatment regime to differentiate the hESCs (H9) by removing FGF-2 from and adding retinoic acid (RA) to the culture medium. Four replicates of self-renewing (H9self) and differentiating (H9diff) hESCs were used for RNA-seq and Ribo-seq analyses. b Expression heatmap of pluripotency (blue) and lineage (red) markers measured by RNA-seq and Ribo-seq. Expression is shown as log2 difference to the mean. Markers in each group are ordered by decreasing expression. c, d MA plots showing the log2 fold change of differentiated (diff) versus self-renewing (self) hESCs against mean expression in either RNA-seq (c) or Ribo-seq (d). Examples of significant genes related to differentiation are shown in red. e–g RT-qPCR confirming similar change in RNA levels of pluripotency markers (upper panels) and lineage markers (lower panels) in hESCs RA-differentiated for 5 days (e) and in embryoid bodies grown for 5 days (f) or 7 days (g). Shown is the mean (n = 3–4). Error bars s.d.