Fig. 3

Chromatin accessibility of SN4741 cells do not resemble ex vivo dopaminergic neurons. A SN4741 samples are highly correlated with each other but very poorly correlate with the open chromatin landscape of either midbrain (MB) or forebrain (FB) embryonic mouse dopaminergic neurons. B Principal component analysis shows a clear separation between the ex vivo and in vitro samples along PC1, representing 86% of the variance. C An upset plot and associated Venn diagram quantify the overlap of peaks between the four conditions and show the poor relationship between the SN4741 cells and the ex vivo mouse dopaminergic neurons. Most peaks are specific to a single cell type/temperature or are restricted to either the ex vivo or in vitro samples. Few peaks are specifically shared between the non-permissive temperature and the ex vivo samples; for example, there are just 183 peaks that are shared exclusively by the MB dopaminergic neurons and the SN4741 cells at the non-permissive temperature. D A genome track showing the normalized read pile up and called consensus peaks in each of the cell types/temperatures at the key dopaminergic neuron specification gene, Th. The chromatin accessibility is largely similar within ex vivo or in vitro cells but bear little resemblance to each other