title: Aspen 7K Array version 2.1
status: Public on Jan 21 2010
contact.city: Athens
contact.first: Chung-Jui
contact.last: Tsai
contact.email: cjtsai@uga.edu
contact.state: GA
contact.address: 120 Green Street
contact.department: School of Forestry and Natural Resources
contact.country: USA
contact.institute: University of Georgia
organism: Populus
manufacture_protocol: 1. Array design: The second generation aspen 7K array contains replicate subarrays of 6,705 elements in a 4×4 grid with a spot diameter of ~150 μm and a spacing of 200 μm. These elements represent ~5,400 unique JGI Populus gene models, and include various positive and negative controls (Lucidea Universal ScoreCard, Amersham) to monitor target labeling and hybridization efficiency, as well as many known function genes derived from our previous and ongoing research.  2. Print area: The replicate subarrays occupy an approximately 18×37 mm area on the non-barcode side.  Spots were printed with Corning Pronto! spotting solution at the Genomics Technology Support Facility of Michigan State University.   3. Spot layout: Each grid contains 12 spike controls on the top left corner. These include calibration controls (from high to low concentrations), ratio controls (different ratio combinations between Cy3 and Cy5 targets), and negative controls. Each grid contains 21×21 spots, except for the last row which has variable number of empty spots.  4. Spikes: To take advantage of the spike controls, appropriate spike mRNA samples need to be included during target labeling (see Amersham manual). However, the use of spike mRNA in hybridization is optional, and will not affect the array analysis (e.g., using global per chip normalization etc).  5. Clone information: ESTs were obatined from Populus tremuloides (Ranjan et al. 2004) or Populus fremontii x angustifolia. Sequence information can be obtained by searching the GenBank or our ESTdb (http://aspenDB.uga.edu) using the MTU clone IDs. As is the case for other large-scale projects, there are likely errors in the annotation.  6. This platform contains a non-redundant clone list from the full array (GPL6992).  Duplicate spots (EST clones in the subarrays or spike controls) are represented only once.                             Ranjan P, Kao Y-Y, Jiang H, Joshi CP, Harding SA, Tsai C-J (2004) Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) trees altered in phenylpropanoid metabolism. Planta 219: 694-704.