In Extended Data 4f, epigenomes were first grouped by methylation platform, and then ordered by Fig. 2a within each platform. The chromatin state methylation profiles in the cell lines vs primary cells/tissue cells were analyzed using a mixed model with repeated measures. Overall effect of the group (cell lines vs primary cells/tissue cells) was tested using epigenomes within group as the error term. Bonferroni correction was used for adjusting the p-values.
