Fig. 1

Experimental and data analysis workflows to evaluate CUT&RUN from fresh and frozen samples. A Experimental process used to compare fresh and frozen cell isolates for CUT&RUN analysis for histone modification and transcription factors. B Data analysis workflow for ssvQC package. Arrows show the order of the steps. Data preprocessing steps are indicated in salmon color and ssvQC output files are grouped in yellow color. Shown are representative ssvQC output files, including summaries of overlapping peak sets via binary heatmap or Euler plots, clustered heatmap of CUT&RUN signal at peak regions, and strand cross correlation (SCC) analysis showing estimated fragment length (blue line) and read length (red line)