title: Rice japonica 400K NimbleGen Oligo Array
status: Public on Feb 06 2007
contact.city: New Haven
contact.first: Xiangfeng
contact.last: Wang
contact.email: bryan4587@hotmail.com
contact.state: CT
contact.address: 352 OML, 165 Prospect st
contact.department: MCDB
contact.country: USA
contact.institute: Yale University
contact.phone: 2035084833
organism: Oryza sativa
description: gene level expression array, contain 400k oligos, based on gene models from TIGR v3 build
manufacture_protocol: 1. Oligo length: 36.
  2. Maximum distance accepted between the 5' end of the oligo and the 3' end of the input sequence: 2000
  3. Minimum oligonucleotide Tm: 80.
  4. Maximum oligonucleotide Tm: 95.
  5. Temperature to use during secondary structure prediction (an oligo will be rejected if it can fold into a stable secondary structure at this temperature): 65,
  6. Threshold to report putative cross-hybridizations (all targets hybridizing with a given oligo with a Tm exceeding this threshold are reported): 70,
  7. Minimum oligonucleotide GC content: 40.
  8. Maximum oligonucleotide GC content: 73 for gene models; 77 for TARs.
  9. Minimum distance between the 5' end of two adjacent oligos: 1.