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G4-ChIP-seq_HepG2.mdG4-ChIP-seq_HepG2.md  
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G-quadruplexes are transcription factor binding hubs in human chromatin

This repository contains all relevant data access and computational analyses .

Data

  • All in-house sequencing data have been deposited in the NCBI GEO database under accession number GSE145090.

  • Additional replicates for G4 ChIP-seq in K562 cells have previously been deposited in NCBI GEO GSE107690.

  • G4 forming sequences in genomic (OQS), single-stranded DNA observed via G4-seq are available in NCBI GEO GSE63874.

  • DNase-seq data for open chromatin maps and ChIP-seq maps of transcription factors and histone marks in K562 cells were downloaded from ENCODE ENCSR000EOT. Files were mapped to hg19 in Jan 2019. The meta data of the considered ChIP-seq files can be found here.

  • RNA-seq data for K562 cells were downloaded from ENCODE ENCSR000AEM and ENCSR545DKY

Code

  • BG4 ChIP-seq analysis and G4 control data set in K562 and HepG2 cells

  • Genomic association testing

  • Expression analysis

Tools

Tool version URL
cutadapt 1.16 http://cutadapt.readthedocs.io/en/stable/installation.html
BWA 0.7.15 http://bio-bwa.sourceforge.net/
Picard 2.14.0 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
samtools 1.6 http://www.htslib.org/download/
Deeptools 3.1.2 https://deeptools.readthedocs.io/
PAVIS Accessed Jan 2019 to Dec 2019 https://manticore.niehs.nih.gov/pavis2/
MEME-ChIP Accessed Jan 2019 to Dec 2019 http://meme-suite.org/tools/meme-chip
GAT 1.3.5 https://gat.readthedocs.io
Intervene 0.6.4 https://github.com/asntech/intervene
FIMO 4.1.12 http://meme-suite.org/doc/fimo.html

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