TL;DR
The genome-wide profiling of histone modifications by CUT&Tag in cancer tissues, a relatively new method for profiling diverse chromatin components, is described.
A detailed CUT&RUN protocol from sample collection through data analysis, including best practices and defined controls to ensure specific, efficient, and robust target profiling is provided.
The protocols for ChIP-seq are outlined, including immunoprecipitation, library preparation for high-throughput sequencing, and bioinformatics analysis of sequencing data that the authors routinely perform in their lab groups, and include troubleshooting tips for each step.
This chapter describes an optimized in situ Hi-C protocol tailored for cancer cell lines using MboI digestion and biotin-mediated pull-down to generate high-complexity libraries and outlines a computational workflow that extends beyond standard topological mapping of compartments and topologically associating domains t...
Extracellular chromatin fragments, including cell-free DNA (cfDNA) and histones, have emerged as promising non-invasive biomarkers for cancer screening and monitoring. While aberrant DNA methylation patterns in cfDNA are already established hallmarks of cancer and are increasingly used in liquid biopsy assays, circulat...
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