ChIP-seq Analysis Pipeline for H3K27ac and H3K4me1/3

ChIP-seq analysis was carried out as described previously (Wiseman et al., 2015 (link)). OE19 H3K27ac and GAC H3K4me1/3 ChIP-seq reads were mapped to the human genome GRCh38 (hg38) using Bowtie2 v2.3.0 (Langmead and Salzberg, 2012 (link)). Biological replicates were checked for concordance (r > 0.80). Peaks were called using MACS2 v2.1.1, using input DNA as control (Zhang et al., 2008 (link)). Mapped reads (≥q30) were retained using SAMtools (Li et al., 2009 (link)). Reads mapping to blacklisted regions were removed using BEDtools (Quinlan and Hall, 2010 (link)).

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Ahmed I., Yang S.H., Ogden S., Zhang W., Li Y, & Sharrocks A.D. (2023). eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways. eLife, 12, e80840.

Publication 2023

Biological Chip seq Human Human genome

Corresponding Organization :

Other organizations : University of Manchester

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Variable analysis

independent variables

ChIP-seq analysis method (as described previously)
Genomic regions (OE19 H3K27ac and GAC H3K4me1/3)

dependent variables

ChIP-seq read mapping to the human genome GRCh38 (hg38)
Concordance between biological replicates (r > 0.80)
Peaks called using MACS2 v2.1.1

control variables

Input DNA used as control for peak calling with MACS2

controls

Input DNA as a negative control for peak calling

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