Fig. 3: Comparison of H3K27ac FFPE-CUTAC to FACT-seq and CUT&Tag of frozen unfixed samples.
From: Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag
a–d IGV tracks showing representative examples of housekeeping gene regions were chosen to minimize the effect of cell-type differences between FFPE-CUTAC (three brain tumors) and published FACT-seq and control CUT&Tag data (kidney). Forebrain H3K27ac ChIP-seq and ATAC-seq samples from the ENCODE project are shown for comparison, using the same number of fragments (20 million) for each sample. Also shown are tracks from FFPE-CUTAC samples using an antibody to RNAPII-Ser2,5p. A track for Candidate cis-Regulatory Elements (cCREs) from the ENCODE project is shown above the data tracks, which are autoscaled for clarity. e, f Number of peaks and Fraction of Reads in Peaks (FRiP) called using MACS2 on samples containing the indicated number of cells. g Cumulative log10 plots of normalized counts from 10 million mapped fragments intersecting cCREs versus log10 rank. Source data are provided as a Source Data file.
