A NimbleGen 2.1M feature long oligo array (OID29684) was designed using B73 RefGen2 assembly, masked for repetitive sequences (J. Stein and D. Ware)  and then used to tile probes every 200bp (except  on chromosome 9 where we selected additional probes tiled every 56bp to improve resolution).  In addition, 35,000 control probes that match maize genomic DNA characteristics were selected  to provide estimates of noise.