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A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5' ends of genes.

Motivation: Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms.

The Affymetrix GeneChip Human Exon 1.0 ST Array is a dense microarray designed for GEP, featuring 6.5 million probes corresponding to known targets and predicted exons spanning the entire human genome [ 7].

Although many promoters featured on this microarray design are expected to be active in multiple tissues and stages of development, it should be noted that most comprehensive results will be obtained with this design when analyzing promoter binding events in gastrula stage embryos.

After initial screening, unique probes showing no cross-hybridisation potential were selected to produce an 8 × 15 K Agilent custom oligo-DNA microarray design format (Agilent Design ID = 038391), comprising 15,208 user defined features and 536 Agilent positive and negative controls.

In addition, all scaffolds of the whole-genome tiling microarray design were randomly distributed over the 5 microarrays of the array set to prevent that any single microarray features all the small scaffolds.

Improvements in microarray design now allow rapid fabrication of custom microarrays, representation of an increasingly large number of features on a single glass slide and hybridization of multiple samples on physically separated arrays on the same slide.

Microarray design has been described previously [39].

Microarray design and hybridization.

Each microarray included approximately 100 features of serially diluted chromosomal DNA 15-200 replicates of each dilution) isolated from the same strain used for the microarray design (MG1655).

BK contributed to microarray design and printed the microarrays.