title: Agilent-020164 Yeast genomic 44K tiling Microarray [Cairns-RSC-ISWI-44K]
status: Public on Mar 31 2015
contact.city: Salt Lake City
contact.first: Timothy
contact.middle: J
contact.last: Parnell
contact.email: timothy.parnell@hci.utah.edu
contact.state: UT
contact.address: 2000 Circle of Hope
contact.country: USA
contact.institute: Huntsman Cancer Institute
organism: Saccharomyces cerevisiae
description: The column 'Chr_coordinate' represents the original coordinates based on the SGD (Saccharomyces Genome Database) genome release version 55 to which the array was originally designed. These coordinates are also listed in the raw Agilent text data files.
  The RANGE_START, RANGE_End columns represent the coordinates based on the recent and stable genome version 64 (equivalent to UCSC SacCer3) and the coordinates used in GSE65591 study.
manufacture_protocol: The HybMap microarray was custom designed to represent genes with a range of RSC and ISW1 occupancies, and included 448 coding genes, 93 tRNA genes, and 52 non-coding genes. Gene regions were extended by either 300 bp (coding and non-coding) or 150 bp (tRNA). Probes were selected from a pool of tiled 60mers and adjusted for length to match melting temperatures as necessary. Both strands for each probe were included in the design. Probes have a mean spacing of ~ 50 bp. As a control, 502 probes with sequences from zebra fish were included as non-hybridizing control probes; sequences were confirmed not to have significant homology to yeast sequences.