ChIP-seq was performed using ChIPmentation (12 (link)) with the following antibodies: CTCF (2899S), H3K27me3 (9733S), and H3K27ac (8173S) from Cell Signaling Technology and H3K4me3 (ab1012) from Abcam. Sequencing was performed on a NovaSeq 6000 (Illumina, San Diego, CA) to obtain ~50 million 150 bp paired-end reads. Data were analyzed via adapter trimming with trimgalore and alignment to GRCh38 using bwa mem (13 ). Normalized coverage for visualization and analysis used the deeptools ‘bamCoverage’ tool (14 (link)), and peaks were called with macs2 (15 (link)) for CTCF and epic2 (16 (link)) for histone marks. Statistical comparisons with DESeq2 (17 (link)) used raw fragment counts at peak summits and visualizations were prepared with Gviz (18 ).
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ChIPmentation: Comprehensive Epigenomic Profiling
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Corresponding Organization : James S. McDonnell Foundation
Other organizations : Washington University in St. Louis
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Variable analysis
independent variables
- Antibodies used: CTCF (2899S), H3K27me3 (9733S), H3K27ac (8173S) from Cell Signaling Technology, and H3K4me3 (ab1012) from Abcam
- Enrichment of CTCF, H3K27me3, H3K27ac, and H3K4me3 binding sites
- Genome used for alignment: GRCh38
- Sequencing platform: NovaSeq 6000 (Illumina, San Diego, CA)
- Sequencing depth: ~50 million 150 bp paired-end reads
- Data analysis tools: trimgalore for adapter trimming, bwa mem for alignment, deeptools 'bamCoverage' for normalized coverage, macs2 for CTCF peak calling, epic2 for histone mark peak calling, and DESeq2 for statistical comparisons
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