Figure 3

Results from manual and automated multiplexed lobChIP runs. a Motifs identified de novo for seven TFs from the manual 1-day lobChIP experiment, with the number of identified peaks and percentage of peaks overlapping (within 1 kb) with ENCODE peaks. (Asterisk) For NRF1 where more peaks were identified in our dataset, the percentage of ENCODE overlapping with our peaks is given. b Normalized signals (RPM) for H3K36me3, Pol II and TFs over the TBC1D4 gene with an enlarged region illustrating motif positions and peaks for FOXA1/2, TCF7L2 and HNF6 at distinct locations. c Automated lobChIP results for FOXA1 give an enrichment profile similar to the ENCODE sample, as exemplified here for the APOA5–APOA1 region. d Venn diagram for FOXA1 overlaps for automated lobChIP (blue) and standard ChIP-seq protocols on the SOLiD instrument [8] (red). e Venn diagram of overlaps between genes with enrichment for H3K4me3 in the AHT-ChIP-seq study (blue) and in the automated lobChIP run (green).