ChIP assays detect Dichaete binding. Binding profiles of Dichaete in the early embryo (stage 5) generated by the Berkeley Drosophila Transcription Network Project  are shown in each graph with bound regions identified at 1% and 25% FDR shown as black bars above the ChIP profile. The grey bars represent 1% and 25% FDR regions identified by modENCODE (embryonic stages 1–12). The location of each amplicon assayed by specific ChIP-PCR assays is indicated by the numbered grey boxes below the GBrowse gene model for each region. Gene models above the chromosome scale line are transcribed from left to right and those below from right to left as indicated by the arrows in the introns. The PCR enrichments from anti-Dichaete and control immunopurification reactions are shown in the gel images below the gene models with the numbers indicating the amplicons. A) Approximately 55 kb encompassing the sli gene. The location of the known sli midline enhancer (fragment 13) is indicated by an asterisk and a grey bar above the gene model. B) 25 kb around the ase gene. C) 25 kb around comm.