Part I: DNA Methylation
1.Generating sequencing-based DNA methylation maps from low DNA input samples
Suzan Al Momani, Euan J. Rodger, Peter A. Stockwell, Michael R. Eccles and Aniruddha Chatterjee
2.Data analysis of DNA methylation Epigenome-Wide Association Studies (EWAS); A guide to the principles of best practice
Basharat Bhat and Gregory T. Jones
3.Next-generation bisulfite sequencing for targeted DNA methylation analysis
Jim Smith, Robert Day and Robert J. Weeks
4.Editing of DNA Methylation Patterns Using CRISPR-Based Tools
Jim Smith, Rakesh Banerjee, Robert J. Weeks and Aniruddha Chatterjee
5.Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling
Allegra Angeloni, James Ferguson and Ozren Bogdanovic
Part II: Protein-DNA interactions
6.Chromatin immunoprecipitation sequencing (ChIP-seq) protocol for small amounts of frozen biobanked cardiac tissue
Jiayi Pei, Noortje AM van den Dungen, Folkert W Asselbergs, Michal Mokry and Magdalena Harakalova
7.A robust protocol for investigating the cohesin complex by ChIP-sequencing
Macarena Moronta Gines and Kerstin S. Wendt
8.Epi-Decoder: decoding the local proteome of a genomic locus by massive parallel chromatin immunoprecipitation combined with DNA-barcode sequencing
Maria Elize van Breugel and Fred van Leeuwen
9.A protocol for studying transcription factor dynamics using fast Single-Particle Tracking and Spot-On model-based analysis
Asmita Jha and Anders S. Hansen
10.Characterization of mammalian regulatory complexes at single locus resolution using TINC
Anja S. Knaupp, Ralf B.Schittenhelm and Jose M. Polo
11.Profiling protein-DNA interactions cell-type-specifically with Targeted DamID
Owen J. Marshall and Caroline Delandre
12.Genome-wide mapping and microscopy visualization of protein-DNA interactions by pA-DamID
Tom van Schaik, Stefano G. Manzo and Bas van Steensel
13.The dCypher approach to interrogate chromatin reader activity against post-translational modification-defined histone peptides and nucleosomes
Matthew R. Marunde, Irina K. Popova, Ellen N. Weinzapfel, and Michael C. Keogh
Part III: Chromatin accessibility
14High-resolution ATAC-seq analysis of frozen clinical tissues
Paloma Cejas and Henry W. Long
15 Single-molecule multikilobase-scale profiling of chromatin accessibility using m6A-SMAC-seq and m6A-CpG-GpC-SMAC-seq
Georgi K. Marinov, Zohar Shipony, Anshul Kundaje, and William J. Greenleaf
Part IV: Genome structure and organisation
16 Circular chromosome conformation capture sequencing (4C-seq) in primary adherent cells
Judith Marsman, Robert C. Day and Gregory Gimenez
17 Mammalian Micro-C-XL
Nils Krietenstein and Oliver J. Rando
18 In situ HiC
Timothy M. Johanson and Rhys S. Allan
19 LncRNA-chromatin pull-down using biotin-conjugated DNA probes
Debina Sarkar and Sarah D. Diermeier
20 Super-resolution microscopy for visualization of physical contacts between chromosomes at nanoscale resolution
Zulin Yu and Tamara A. Potapova
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