Chapter 2 42 replicates (Fig. 1B). Hierarchical clustering showed that samples in both analyses group by cell type. Colour coding indicates that iPSCs and cerebellar cells are more closely related to the relevant ENCODE profiles, than the other cell types (iPSCs = P < 0.001; cerebellar cells = P < 0.001). Taken together, fibroblast-derived iPSCs and PSC-derived cerebellar cells can be treated as relevant representatives of those developmental stages/lineages for further analyses. Figure 1. Reprogramming and differentiation leads to distinct cell types. (A) shows the projection of 23 samples in 2-dimensional space. Each dot represents a sample that is labelled according to patient/control status. Samples are positioned based on relative similarity, showing that fibroblasts, iPSCs and cerebellar cells cluster together. (B) Heat maps of the comparison of expression profiles with ENCODE iPSC and granule cell samples. The heat map represents Spearman’s rank correlation coefficient. Patient/control status and cell types are indicated at the top of the heat map. C = control; F = fibroblast; G = cerebellar granule cell; I = iPSC; P = patient.
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