title: NimbleGen/SNU Rice 3'-tiling 385K array
status: Public on Jul 07 2010
contact.city: Seoul
contact.first: Ju-Seok
contact.last: Seo
contact.email: tin3725@hanmail.net
contact.address: san 56-1
contact.department: Dept. of Applied Biology & Chemistry
contact.country: South Korea
contact.institute: Seoul National University
contact.phone: 82-2-880-4659
organism: Oryza sativa
description: The profiling was conducted with the Rice 3'Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp).
  Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon and with shifting 10 bp so 10 probes cover 150 bp in the 3' region of the gene.
  Genes from chloroplast (123) and mitochondria (74) and selection markers such as gfp, gus, hyg, bar, and kan are included. In total, 270,000 probes were designed with the average size of probe is 60-nt long to have its Tm value 75 to 85 °C.
manufacture_protocol: The microarray was manufactured at NimbleGen inc (http://www.nimblegen.com/). Random GC probes (38,000) to monitor the hybridization efficiency and four corner fiducial controls (225) were included to assist with overlaying the grid on the image.