title: Agilent-027438 Yeast S-Y SNP v1 [Probe Name Version]
status: Public on May 05 2015
contact.city: Durham
contact.first: Thomas
contact.middle: D
contact.last: Petes
contact.email: tom.petes@duke.edu
contact.state: NC
contact.address: 213 Research Drive
contact.department: Molecular Genetics and Microbiology
contact.country: USA
contact.institute: Duke University School of Medicine
contact.phone: 919 684-4986
organism: Saccharomyces cerevisiae
description: Whole genome SNPs between S288c and YJM789. Both Watson and Crick strands represented as well as both probes specific to both strains.
  
  In the labels of the oligonucleotides 'SF', 'SR', 'YF' and 'YR' refer to the orientation and origin of the sequences used for the oligonucleotides on the microarrays. 'S' and 'Y' indicate whether the oligonucleotide contains sequences identical to the reference S288c genome (closely related to W303-1A) or the YJM789 genome, respectively. 'F' and 'R' indicate whether the orientation (5' to 3') is identical to the orientation in SGD ('F' standing for forward) or opposite to that shown in SGD ('R' for reverse). Thus, 'F' and 'R' have the sequences of the complementary Watson and Crick strands at each position. For all oligonucleotides for a particular SNP, the number used to label the coordinate is the coordinate of the first base of the oligonucleotide in the 'F' orientation. In addition, the oligonucleotides for the YJM789-derived sequences were labeled with the same coordinate as the S288c-derived sequences. The sequence information for the YJM789 sequences was from SGD based on the paper by (Wei et al., 2007. PNAS 104:12825-12830).
  
  Arrays of this design have barcodes that begin with 16027438 or 2527438.
  
  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 Feature Extraction feature number.
  
  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/