AI Networking Cookbook: Practical recipes for AI-assisted network automation and development
TL;DR
This chapter describes the experimental setup and provides a detailed protocol for performing chromatin immunoprecipitation in Ustilago maydis or related smut fungi.
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.
HisTrader is presented, a computational approach that identifies nucleosome-free regions (NFRs) within ChIP-based profiling of histone modification peaks, which reduces the target sequence length for motif discovery and genetic variant prioritization.
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.
A proximity-labeling protocol for identifying the chromatin-dependent protein interactome associated with specific chromatin marks, termed ChromID, which preserves native chromatin organization and captures transient chromatin-associated interactions that are often lost during conventional affinity purification workflo...
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