Figure 1: Ion Torrent and Illumina HiSeq ChIP-seq.

(a) Density profiles of H3K4me3 (left) and Pol-II ChIP-seq (right) from 2 million Ion Torrent reads (purple) and 15 million Illumina HiSeq reads (blue) over the Mx1 gene locus (top) and a larger region spanning the TNF locus (bottom). The scale of the density profile was set to the same level for each pair of samples and is marked. All ChIP-seq experiments were performed with mouse dendritic cells stimulated with lipopolysaccharide (0.1 μg ml⁻¹) for 2 h. (b) A comparison of H3K4me3 (left) and Pol-II (right) ChIP-seq peak enrichment scores (log₂) over a 500-bp sliding window from 2 million Ion Torrent reads (x axis) and 15 million Illumina HiSeq reads (y axis). The Pearson correlation coefficient is marked at the upper right corner. The grey scale represents a two-dimensional density plot, where the grid is divided into hexagonal bins and the colour intensity reflects the density (counts) in the bin. An intensity bar of the counts is shown at the right bottom corner. (c) Saturation analysis to test for sufficient sequencing depth. Shown is the Pearson correlation coefficient (y axis) calculated between decreasing sequencing reads randomly subsampled from the H3K4me3 ChIP-seq Ion Torrent reads (x axis) and either 15 million H3K4me3 ChIP-seq Illumina HiSeq reads (blue) or 2 million Ion Torrent reads (purple). (d) Density profiles of H3K4me3 ChIP-seq from 2 million Ion Torrent reads for libraries with 56, 4 or 0.4 ng of immunoprecipitated input DNA. (e,f) A comparison of H3K4me3 ChIP-seq peak enrichment scores (log₂) over a 500-bp window from 2 million Ion Torrent reads with 56 ng (y axis) and 4 ng (d, x axis) or 0.4 ng (e, x axis) of immunoprecipitated input DNA. The Pearson correlation coefficient is marked at the upper right corner. The grey scale representation as in panel b.