title: Aspen 14k Array 2.1_2007 from MTU
status: Public on Jul 24 2008
contact.city: Gainesville
contact.first: Christopher
contact.last: Dervinis
contact.email: cderv@ufl.edu
contact.state: FL
contact.address: 2033 Mowry Road, rm 320
contact.department: SFRC
contact.country: USA
contact.institute: University of Florida
contact.phone: 352-273-8085
organism: Populus tremuloides
description: http://aspendb.mtu.edu/nsf.phtml
  The Platform data table reflects the fact that the spots were duplicated on the array.
manufacture_protocol: The following was provided by Michigan Tech about the aspen array design:
  The aspen 7K array (2nd generation)
  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.
  3. Spot layout: Each grid contains 12 spike controls on the top
  left corner. The first 5 are calibration controls (from
  high to low concentrations), followed by 1
  negative control , 3 or 5 ratio controls (different
  ratio combinations between Cy3 and Cy5 targets), and another negative control ,or negativeratio-negative controls.  Each grid contains 21×21
  spots, except for the last row which has variable number ofempty spots.
  4. Spikes: To take advantage of the spike controls, appropriate
  spike mRNA samples need to be included during target
  labeling (see Section C below and 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: A gene list can be downloaded from our website (www.aspenDB.mtu.edu).
  Sequence information can be obtained by searching the GenBank or our ESTDB with the MTU clone
  IDs. As is the case for other large-scale projects, there are likely errors in our array system. Due to
  funding limit, we have only re-sequenced a number of randomly selected array-ESTs. Other potential
  errors include mis-annotation, or mis-classification with regard to the functional groups. Therefore,
  additional confirmation for array-selected candidate genes will be necessary.
  References: 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.