Fig. 5
From: Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs
AutoCUT&RUN is suitable for profiling the chromatin landscape of frozen tumor samples. a DMG experimental setup. Two DMG cell lines derived from a similar region of the brainstem were grown as xenografts in the brains of immunocompromised mice, and upon forming tumors were resected and frozen. Xenografts were thawed and processed by AutoCUT&RUN in parallel with control DMG samples harvested directly from cell culture. b Hierarchically clustered correlation matrix of AutoCUT&RUN profiles of histone-H3 modifications that mark active (pink) and repressed (blue) chromatin in VUMC-10 (orange) and SU-DIPG-XIII (purple) cells grown in cell culture (C.C.) or as xenografts (Xeno.). As a quality control, H3K27ac was also profiled manually in these cell lines using a different antibody (*). Pearson correlations were calculated using the log2-transformed values of read counts split into 500Â bp bins across the genome