title: Nimblegen apple 60-mer oligo array (March 2005)
status: Public on May 05 2006
contact.city: University Park
contact.first: Izabela
contact.last: Makalowska
contact.email: izabelam@psu.edu
contact.state: PA
contact.address: 502 Wartik Lab
contact.country: USA
contact.institute: Pennsylvania State University
contact.phone: 814-865-2695
organism: Malus domestica
description: This set includes 60-mer oligonucleotides for 55,155 apple contigs assembled form available apple ESTs  (March 2005) and 75 locally sequences cDNA sequences. EST sequences were assembled  using TIGR TGICL assembly software.  Assembly was done twice,  one for 'gala' variety only (75751 ESTs) and second for all apple (183732 ESTs.) In addition 400 apple mRNA sequences were used as assembly seeds.  Contigs resulting from both assemblies were used for oligo design.
  Gene DNA strand for oligo design was determined using BLASTX against Arabidopsis and NCBI nr databases. Oligos were designed from both strands for  each sequence  with  no significant BLAST hit.
manufacture_protocol: NimbleGen proprietary software used to identify 6 perfectly matched 60-mer oligonucleotides for each apple gene.