title: UT/TH_all-8mer-v1
status: Public on Jun 20 2008
contact.city: Toronto
contact.first: Lourdes
contact.last: Pena-Castillo
contact.email: lourdes.pena@gmail.com
contact.state: Ontario
contact.address: 160 College St. Room 1350
contact.department: Banting and Best Department of Medical Research
contact.country: Canada
contact.institute: University of Toronto
contact.phone: 416 946-7838
organism: synthetic construct
description: This protein binding microarray (PBM) involved binding GST-tagged proteins to custom-designed, double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006.  A key feature is that the microarrays are composed of de Bruijn sequences that contain each 10-base sequence once and only once, providing an evenly balanced sequence distribution. Individual de Bruijn sequences have different properties, including representation of gapped patterns.  The original Berger et al. array sequences  are available via a EULA at http://the_brain.bwh.harvard.edu/UPBMseqn/UPBMseqn_agreement.html.
manufacture_protocol: In situ oligosynthesized array with proprietary synthetic sequences that target all possible 8-base sequences. The sequences shown in the below table are not the actual sequences that are printed on the array.