title: NimbleGen Zea Mays 2.1M array
status: Public on Nov 19 2009
contact.city: Ames
contact.first: Patrick
contact.middle: S.
contact.last: Schnable
contact.email: schnable@iastate.edu
contact.state: IA
contact.address: 2035B Roy J Carver Co-Lab
contact.country: USA
contact.institute: Iowa State University
contact.phone: 515-294-0975
organism: Zea mays
description: Probe sequences were aligned to Maize pseudomolecules from the Arizona Genome Institure (AGI) released on March, 20th, 2009 to determine their positions in the genome (positions are reflected in the Platform data table).
  Due to the fact that our array was designed using B73 genomic sequence and the high rate of polymorphism between B73 and Mo17, the CGH data violated the assumption for the regularly used Q-spline normalization to make two channels of hybridization intensities comparable. We used a subset of 840,289 probes that were known to have identical sequence in B73 and Mo17 (based on B73 BAC sequences and Mo17 WGS data) as a control set to obtain a best-fitting cubic spline function (Workman et al., 2002), assuming that most of these probes should have the same hybridization intensities after normalization. The spline function was then globally applied for all probes to normalize the two channels.  After within-chip normalization, linear model analyses using LIMMA (Smyth 2004; Smyth 2005) were conducted for the data from all microarrays. The linear model for each probe included effects for dyes and genotypes (B73, Mo17, RIL M0022, and RIL M0023), and p-values were calculated to test for a signal difference between Mo17 and B73 genotypes as part of each linear model analysis.
  NimbleGen .ndf array description file linked below as supplementary file.
manufacture_protocol: A high-density (2.1 million feature) oligonucleotide microarray was designed by Roche NimbleGen to perform comparative genomic hybridization (CGH) of maize B73 and Mo17 inbred lines.  A set of 14,423 maize BACs (downloaded March 2008) was used to design isothermal probes, varying in length from 45 bp to 85 bp and with a target Tm of 76C at a fixed interval of 50 bp.  Probe sequences were repeat-masked by calculating the average 14-mer frequency for each probe, based on a frequency table generated from the complete set of BAC sequences available as of that date, and removing probes with an average 14-mer frequency higher than 400. Probe uniqueness was determined by comparing each probe to the B73 reference genome, using SSAHA (http://www.sanger.ac.uk/Software/analysis/SSAHA/) with a step-size of 1, nmer-size of 12 and a minimum match length of 33 bp. Up to five insertions/deletions were allowed in each match. Probes with <=15 close matches in the genome were included in the array design. Median final probe spacing was 450 bp.  It should be noted that this set of probes was designed to facilitate sequence capture (Albert et al., 2007); if NimbleGen's CGH probe design criteria had been utilized it is likely that the choice of probes would have been slightly different. See manufacturer's website for more details.