title: Whole rice locus 44K array 2
status: Public on Nov 27 2007
contact.city: Sapporo
contact.first: Kouji
contact.last: Satoh
contact.state: Hokkaido
contact.address: Hitsujigaoka 1
contact.country: Japan
contact.institute: NARO/HARC
organism: Oryza sativa
description: Keyword: Oryza sativa ssp. Japonica cv. Nipponbare
  Keyword: rice full-length cDNA sequences
  Keyword: TIGR pseudomolecules release 4
manufacture_protocol: For design probes, FL-clone sequences (FLcDNAs and FLESTs) were mapped on TIGR Pseudomolecules release 2 using the BLAT program (determinination of FL-locus)After this mapping, we selected nucleotide sequences from the FL-locus and CDS of TIGR annoatiton release 2 for probe design and about 82K kinds of 60-mer probe candidates were designed by Agilent Technologies on the basis of such factors as GC content and melting Temperature of oligo and were spotted on two slides (41K probes per slide).
  In our investigation, we used the information of TIGR Pseudomolecules release 4 (TIGR4), so, these designed probes were re-mapped on TIGR4 by BLAT according to the criterion (>95% identity, >90% coverage, non-redundant highest score). 63455 probes were mapped on Fl-locus and/or TIGR-locus based on TIGR pseudomolecules release 4.