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

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