ChIP-Chip in Xenopus The files containing the H3K4me3 peaks, the TBP peaks, the number of matches for each probe to X. tropicalis JGI 4.1, as well as the Tilemap parameter files are available as supplementary information through GEO Series GSE19413. scaffolds contain significantly fewer genes and distributing these scaffolds evenly over the 5-array set may prevent signal normalization issues. Arrays featuring these designs can be purchased from Roche Nimblegen. Orphan H3K4me3 Linkage All mapped X. tropicalis ESTs were downloaded from the UCSC Genome Browser (xenTro2, 12-2007). ESTs were filtered based on two criteria: 1) mapping to exactly two scaffolds and 2) a H3K4me3 peak within 1 kb of the EST on one of the scaffolds. All unique combinations of two scaffolds with evidence of more than one filtered EST were kept and are summarized in Table S2. Comparisons between ChIP-Chip Replicates and between ChIP-Chip and ChIP-Seq Peaks To calculate the correlation of the genome-wide replicate to the two replicates on the promoter microarray the mean per-peak log2 ChIP/input signal was calculated per replicate for all the 10,179 peaks. The correlation coefficient between these replicate per-peak signals was calculated using the Pearson’s correlation. To calculate the overlap between H3K4me3 determined by ChIP-chip and ChIP-seq, the H3K4me3 ChIP-seq peaks determined previously (GSM352202_H3K4me3_enriched.bed, available through GEO Series GSE14025) [http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc = GSE14025] were intersected with the peaks deter- mined by ChIP-chip in this study. All ChIP-seq peaks overlapping with at least 1bp were counted as detected by both methods. Data Availability and Supplemental Data The data and the microarray designs used to generate the data have been deposited in NCBI’s Gene Expression Omnibus [22] and are accessible through GEO Series accession number GSE19413 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19413). Improved versions (v2) of the X. tropicalis genome-wide microarray design and the promoter microarray design are available at the authors’ web site (http://www.ncmls.nl/gertjanveenstra). These updated designs include extra control probes (random controls and probes corresponding to Arabidopsis BAC clones F19K16, accession AC011717, and F24B22, accession AL132957). The Arabidopsis sequences can be used as spike-in controls. In addition, all scaffolds of the whole-genome tiling microarray design were randomly distrib- uted over the 5 microarrays of the array set to prevent that any single microarray features all the small scaffolds. The small (high number) References 1. Bennett S (2004) Solexa Ltd. 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