ChIP-Chip in Xenopus amplification protocol [10] and hybridized to a newly designed Nimblegen whole-genome tilepath set of five microarrays covering the complete X. tropicalis genome (Joint Genome Institute v4.1). The microarrays used each consist of 2.1M isothermal (76uC) probes of 50–75bp in length that are spaced by an average of 100 bp in the genome, with the exclusion of repeat-masked regions (Figure 1A). The H3K4me3 signal was present at the 59 end of genes, as is shown for a typical euchromatic genomic region, covering the genes ppil2, ypel1 and mapk1 (Figure 1B). To generate a single promoter microarray design (Figure 1C), all putative H3K4me3 positive regions (27,019 regions, see material & methods for details), together with the 59 ends of all 27,916 Joint Genome Institute FilteredModels genes (22 kb/+2 kb) were selected. In addition, approximately 1,000 regions were included based on clusters of 59 ends of ESTs (22 kb/+2 kb). In total, the promoter microarray design contains 1,951,339 probes, comprised of 46,302 contiguous sequences with a median length of ,4 kb. In addition, to measure genomic background ChIP-chip signals for the purpose of peak detection the contiguous sequence of several scaffolds were included completely. Promoter Microarray H3K4me3 ChIP-Chip Two new H3K4me3 gastrula ChIP-chip samples were gener- ated, amplified using the T7 method and hybridized to the new promoter microarray design. The two biological replicate samples are quite similar in terms of location and shape of the enriched regions as is shown for part of scaffold 1 (Figure 2A). We determined the correlation between the genome-wide ChIP-chip and the promoter ChIP-chip experiments (Figure 2B). The mean signal per peak of the genome-wide experiment correlated with the Figure 1. Whole-genome H3K4me3 ChIP-chip of gastrula embryos. (A) Overview of the whole-genome tile path microarray design. (B) H3K4me3 profile for peptidylprolyl isomerase cyclophilin-like 2 (ppil2), yippee-like 1 (ypel1) and mitogen-activated protein kinase 1 (mapk1) that are enriched with H3K4me3 signals at the 59 end visualized using the UCSC Genome Browser. (C) Overview of the promoter tile path microarray design. doi:10.1371/journal.pone.0008820.g001 PLoS ONE | www.plosone.org 2 January 2010 | Volume 5 | Issue 1 | e8820