title: Agilent-045343 Saccharomyces cerevisiae VinVoile 8x15K
status: Public on Apr 30 2014
contact.city: Montpellier cedex1
contact.first: Jean-Luc
contact.last: Legras
contact.email: jean-luc.legras@inrae.fr
contact.address: 2, place Viala
contact.department: UMR1083, Science pour l'Oenologie
contact.country: France
contact.institute: INRA
organism: Saccharomyces cerevisiae
description: This isothermal melting probes array has been designed from the comparison of genome sequence P3 and RM11.1a according to PMID 22065438.
  
  RM11.1a genome sequence can be obtained at: http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae.3/Home.html
  
  Briefly, the array is built on pairs of probes, with each probe specific to one parent to calculate the hybridization differences between each probes in a pair which is proportional to the allele frequencies. The manner the probes used for the analysis are coded such as:
  SACE-rm11-Chr03_1000412_1000394_1000422_r_P3
  SACE-rm11-Chr03_1000412_1000395_1000422_f_RM11
  where SACE-rm11 is the reference genome, Chr03_1000412 the SNP location, 1000394_1000422 the coordinates of the probe, and P3 or RM11 the name of the ancestral allele.
  
  the array contains 6317 position for which a pair of probes has been designed, 1000 control non allele specific probes, and 300 probes that are deposited 5 times as repeat controls; The minimum distance between SNP is 441. The maximum distance is 54501 between position Chr05 9902429 to 956930, and then 20108 between position Chr07 585434 to 605541
  
  Arrays of this design have barcodes that begin with 16045343 or 2545343.
  
  Orientation:
  Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
  
  The ID column represents the Agilent probe name.
  
  Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
  
  To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
manufacture_protocol: see manufacturer's web site at http://www.agilent.com/