title: CCHMC_Nimblegen_zebrafish_32K_Zv6
status: Public on Sep 01 2009
contact.city: Tampa
contact.first: Saulius
contact.last: Sumanas
contact.email: ssumanas@usf.edu
contact.state: FL
contact.address: 560 Channelside Dr
contact.department: Department of Pathology and Cell Biology
contact.country: USA
contact.institute: University of South Florida
organism: Danio rerio
description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files.
manufacture_protocol: Organism: Danio rerio
  Source: Ensembl and UCSC
  Build: Zv6
  Probe Length: 60mer
  Probes per Array: 385,000
  Feature Size: 16μm x 16μm
  Array Dimensions: 17.4mm x 13mm
  Overall Slide Dimensions: 1" x 3" (25 x 75mm)
  Recommended Storage: Store arrays desiccated at room temperature.
  Catalog Number A6183-00-01
  Design Name 2007-03-01 Zv6 60mer EXP
  Description Danio rerio 1-Plex Array
  Genes 32,292
  Probes/ Target 12
  Features 385,000
  Replicates 1
  from www.nimblegen.com
  Array Synthesis
  NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system. At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays. These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.
  Hybridization
  NimbleGen Systems has developed a proprietary hybridization system, including protocols, buffers, hybridization cassettes, hardware, and temperature control instrumentation that generate highly reproducible and sensitive hybridizations. These protocols have been optimized to require minimum amounts of sample, while providing a hybridization volume that can be continually mixed over the time-course of the incubation. This method generates arrays with extremely high inter-array reproducibility (up to r2>0.99) and very low intra-array coefficient of variation (cv < 12%) across the array surface. In a typical gene expression experiment, each gene is represented by a minimum of 10 and as many as 25 probe-pairs complementary to different portions of the mRNA transcript. This guarantees that at least 10 independent measurements of mRNA concentration are included in the final value for the expression level for the gene, resulting in more reliable and reproducible gene expression calculations. In addition, these 10 to 25 probe-pairs are distributed evenly across the surface of the array. This distribution effectively eliminates problems associated with any local variation in the spatial uniformity or noise in the hybridization, because expression values are derived from a minimum of ten different locations on the array.