TL;DR
A comprehensive ATAC-seq protocol that is utilized by laboratories, along with detailed troubleshooting steps at each point, is outlined in the hopes that it will aid other researchers in utilizing this tool to the fullest capability.
Fiber-seq simultaneously profiles chromatin accessibility, DNA methylation, protein footprints, and genetic variation on single molecules at near—base-pair resolution, revealing how genetic and epigenetic features interact to regulate gene expression and provides a powerful new framework for dissecting immune cell func...
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.
Background: Epigenomics has emerged as an essential field in modern molecular biology, providing a critical layer of gene regulation. DNA methylation, histone modifications and alterations to the chromatin accessibility of DNA have been widely associated with complex diseases including cancer. The most recent developme...
This chapter outlines a comprehensive protocol for joint embedding of chromatin accessibility and transcriptomic data using best practices developed in laboratories, along with detailed parameter tuning at each step to fully leveraging this pipeline.
A detailed protocol for flap-enabled next-generation capture (FENGC), a cost-effective method for targeted, multiplexed enrichment of DNA sequences for epigenetic and genetic analysis.
The biology of active human TE is summarized, state-of-the-art short- and long-read pipelines for TE analysis are surveyed, and their applications in studies of aging, cancer, and other complex diseases are highlighted.
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