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.
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.
Genome-wide localisation of histone variants in Toxoplasma gondii implicates variant exchange in transcriptional control by demarcation of functional chromatin regions
Data table header descriptions
ID
SEQ_ID
Unique chromosome ID followed by the position of the first and last base pair of the chromosome.
CHROMOSOME
Chromosomes IA to XII and TGG. TGG "chromosomes" represent assembled regions of the genome which have not been assigned to a true chromosome.
PROBE_ID
Unique identifier for each oligonucleotide represented on the array.
POSITION
Position of the probe SEQUENCE in the target sequence.
LENGTH
Number of nucleotides in probe sequence.
PROBE_COUNT
Number of times the oligonucleotide probe appears on the array.
Less...
More...