Hi, I was wondering if anyone did a comparison between ChIP-Seq data obtained through NEBnext and Illumina Truseq library prep.
We're seeing huge differences between the two kits (reproducible for two different transcription factors), in particular very low enrichment in high GC regions when using Illumina reagents. The problem is most visible at TSSs, where we see a dip in coverage.
Attaching some plots to illustrate it, ChIP1 and ChIP2 are two different transcription factors, IL is Illumina, NEB NEBnext. The venns show peak-level overlaps, the histograms GC content/peak, the lineplots mean extended read count at TSSs.
We're seeing huge differences between the two kits (reproducible for two different transcription factors), in particular very low enrichment in high GC regions when using Illumina reagents. The problem is most visible at TSSs, where we see a dip in coverage.
Attaching some plots to illustrate it, ChIP1 and ChIP2 are two different transcription factors, IL is Illumina, NEB NEBnext. The venns show peak-level overlaps, the histograms GC content/peak, the lineplots mean extended read count at TSSs.
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