title: [BradiAR1b520742] Brachypodium tiling arrray v1.0
status: Public on Oct 01 2012
contact.city: Ghent
contact.first: Stefanie
contact.last: De Bodt
contact.address: Technologiepark 927
contact.country: Belgium
contact.institute: VIB/UGent
organism: Brachypodium distachyon
description: CDF and array design files can be accessed at http://ftp.brachypodium.org/files/Affymetrix/Current/
manufacture_protocol: The Affymetrix array design is based on the DOE-JGI genome sequence of Brachypodium distachyon accession Bd21, Illumina- and EST-based empirical transcriptome analysis, and ab initio gene predictions. A pooled cDNA library from Brachypodium distachyon was sequenced using the Illumina platform and generated ~289 million RNA-seq reads, which were mapped onto the Brachypodium genome assemblies to empirically identify exons and splice junctions (http://www.brachypodium.org/). The array design employs a perfect match (PM) probe strategy using Affymetrix’s 5 micro 49-format array platform containing ~6.5 million features. All of the oligonucleotide probes are unique, single copy sequences within the genome. The mean probe spacing is 42 bases with 95% of probe pairs <126 nucleotides apart. The probes designed for genic regions include 2,548,624 probes targeting exons and introns. On average, exons and introns are represented by 11 probes with 95% of exons or introns targeted by greater than 5 probes. The array also includes 1,062 control probes, 2,050 reporter probes, and 33,886 antigenomic surrogate mismatch probes.