Differential enhancers in murine stem cell differentiation. a Differential enhancer regions of pluripotent (mESC +, gray) and differentiated (mESC −, orange) cells are colored by their respective enhancer probabilities. All regions can be divided into two clusters according to their differential activity pattern. Count distributions of HM ChIP-seq and ATAC-seq read counts recapitulate the dynamic behavior in both clusters. The same trend can also be observed when using a less sensitive setting in the test statistic with a minimum group difference of w0=0.1 (default: w0=0.5). b An example for a dynamic enhancer region (chr8: 26,843,601– 26,845,600, highlighted in blue) which was predicted to be active in the differentiated mESC − but not in the pluripotent mESC +. c The predicted differential enhancer sequence was tested using an enhancer reporter assay (STARR-qPCR). The difference in the transcript levels of the GFP reporter between mESC − (−LIF/+RA) and mESC + (+LIF/ −RA) as well as compared to an untreated sample (−LIF/ −RA) recapitulates the predicted dynamic activity. The LIF-inducible viral enhancer CMV serves as a positive control. As a negative control, we chose nc1, which is not active in mouse embryonic stem cells.