Supplementary Figure 7: Evidence of high-resolution patterns in ChIPmentation data | Nature Methods

Supplementary Figure 7: Evidence of high-resolution patterns in ChIPmentation data

From: ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

Supplementary Figure 7

(a) Tn5 transposase insertion frequencies for ChIPmentation (blue), ATAC-seq signal (green), and DNase-seq signal (red) at ChIP-seq peaks for CTCF, GATA1, PU.1, and REST, centered on the corresponding binding motifs. Signal from tagmented genomic DNA (Nextera genomic DNA library) is displayed in black, indicating inherent sequence bias of the tagmentation enzyme. Signals were averaged over all peaks, smoothed with a 20 bp Hanning window, and Z score transformed for better comparability.

(b) Normalized ChIPmentation (blue) and ATAC-seq (green) signal at ChIP-seq peaks for CTCF, GATA1, PU.1, and REST, centered on the corresponding binding motif. ChIPmentation and ATAC-seq signals were normalized against the signal observed for tagmentation of genomic DNA (Nextera genomic DNA library), in order to correct for the sequence bias of the tagmentation enzyme. Signals were averaged over all peaks, smoothed with a 20 bp Hanning window, and Z score transformed for better comparability.

(c) Frequency of pairwise distances between insertion events (5’ position of reads) in ChIPmentation data for H3K4me3.

(d) Average signal intensity (insertion frequencies) for H3K4me1 ChIPmentation data around centers of nucleosomes (dyads) positioned using the NucleoATAC software (https://github.com/GreenleafLab/NucleoATAC) with ATAC-seq data from GM12878 cells. Note the structured pattern with higher and periodical insertions at the nucleosome borders.

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