DNA G-quadruplex structures mould the DNA methylome

This repository contains data access and computational analysis for the methods developed in our published manuscript.

Data

• All in-house the sequencing data have been deposited in the NCBI GEO database under accession number GSE107690.

• ENCODE's K562 cell line datasets used are as below:

Dataset	Data Type	URL
K562 DHSs	DNase-seq	https://www.encodeproject.org/experiments/ENCSR000EPC/
K562 DNMT1	ChIP-seq	https://www.encodeproject.org/experiments/ENCSR987PBI/
K562 WGBS	Whole Genome Bisulfite Sequencing	https://www.encodeproject.org/experiments/ENCSR765JPC/

• CGI were downloaded using the UCSC’s table browser. Also, as an alternative CpG Island definition, we used CpGCluster

Code

• BG4 ChIP-seq analysis
• Analyses of methylation at promoters and CpG Islands
• Enrichment analysis
• Monte Carlo Simulation
  • Monte Carlo P-value calculation
• Whole genome bisulfite sequencing in HaCaT cells
  • Read processing, alignment and de-duplication
  • Methylation extraction, aggregation and filter by coverage
  • Analysis of methylation changes in BG4 ChIP-Seq peaks, CGIs and promoters before and after Entinostat treatment

Tools

Tool	version	URL
cutadapt	1.15	http://cutadapt.readthedocs.io/en/stable/installation.html
BWA	0.7.15	http://bio-bwa.sourceforge.net/
Picard	2.8.3	http://broadinstitute.github.io/picard
MACS	2.1.1	http://liulab.dfci.harvard.edu/MACS/
Bedtools	2.26.0	http://bedtools.readthedocs.io/en/latest/content/overview.html
Deeptools	0.7.15	https://deeptools.readthedocs.io/
Bismark	0.19.0	https://www.bioinformatics.babraham.ac.uk/projects/bismark/
Liftover	Accessed Aug 2017 to April 2018	http://genome.ucsc.edu/cgi-bin/hgLiftOver