Skip to main content
. 2012 Jun 18;122(7):2519–2530. doi: 10.1172/JCI62613

Figure 1. In vitro validation of ChIP-seq datasets.

Figure 1

(A) Overlap of all ChIP-seq binding regions with genes in refGene plus their promoters, defined here as the 1-kb upstream region of those genes. Values are percentage of all peaks. See Methods for a detailed description of peak definition. (B) Results obtained from the MEME motif discovery analysis. Binding motifs were in good agreement with those recently published for the HL-1 based ChIP-seq (35) and JASPAR motifs. (C) Number of overlapping binding regions between heart-derived ChIP-seq datasets. (D) ChIP-qPCR assay validating ChIP-seq peaks. Regions were randomly chosen from the group of ChIP-seq peaks that showed overlap between ChIP sequencing datasets for TBX3, GATA4 and NKX2-5. Shown is enrichment relative to Hprt for NKX2-5, GATA4, and TBX5 in WT adult mouse hearts and for TBX3 in TBX3-induced adult hearts. Ratios below represent the proportion of peaks that showed relative enrichment of more than 10. (E) Of the regions tested with ChIP-qPCR, 11 were tested for their response to NKX2-5, GATA4, and TBX5 or TBX3 in Cos7 cells. All enhancers responded to stimulation with GATA4 and NKX2-5. *P < 0.05.