title: Toxoplasma gondii ME49 ChIP-chip genome-wide tiling array 1 of 2
status: Public on May 16 2012
contact.city: Tampa
contact.first: Kami
contact.last: Kim
contact.email: kamikim.usf@gmail.com
contact.state: FL
contact.address: 3720 Spectrum Blvd, Suite 304
contact.department: Internal Medicine Medicine
contact.country: USA
contact.institute: University of South Florida
contact.phone: 813 974 5936
organism: Toxoplasma gondii ME49
description: Tiling microarray encompassing 63 Mb of Toxoplasma gondii genome (reference genome strain ME49; chromosomes Ia, Ib, II, III, IV, V, VI, VIIa, VIIb, VIII, IX, X, XI and XII, and unmapped contigs).
  The genome wide chip was designed using the Nimblegen isothermal protocol design based upon Release 4.1 of the T. gondii ME49 genome (www.toxodb.org). The "target Tm" for all probes is 76 C. There are 392,074 probes total on each array for a total of 784,148 probes, including controls. Of these, 366,336 are T. gondii specific probes on each of two slides, Tiling1 and Tiling2 for a total of 732,672 toxo specific probes. The design name for each chip is 2007-05-02_Toxo_WG_tiling1 and 2007-05-02_Toxo_WG_tiling2.
  Genomic sequence available at: http://toxodb.org/common/downloads/release-4.1/
  Native NimbleGen files (ndf, pos) are linked below as supplementary files.
manufacture_protocol: 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 up to 786,000 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 up to 786,000 unique probe features are synthesized in a single array.