title: FHCRC chicken 13K
status: Public on Jan 21 2006
contact.city: Ames
contact.first: Susan
contact.middle: J
contact.last: Lamont
contact.email: sjlamont@iastate.edu
contact.state: IA
contact.address: 2255 Kildee Hall
contact.department: Animal Science
contact.country: USA
contact.institute: Iowa State University
organism: Gallus gallus
description: Background
  The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes.
  
  Results
  We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162) from immune tissues and a chicken bursal cell line (DT40). Quality control analysis indicates there are 13,007 useable features on the array, including 160 control spots. The array provides broad coverage of mRNAs expressed in many tissues; in addition, clones with expression unique to various tissues can be detected.
  
  Conclusions
  A chicken multi-tissue cDNA microarray with 13,007 features is now available to academic researchers from genomics@fhcrc.org. Sequence information for all features on the array is in GenBank, and clones can be readily obtained. Targeted users include researchers in comparative and developmental biology, immunology, vaccine and agricultural technology. These arrays will be an important resource for the entire research community using the chicken as a model.
manufacture_protocol: BBSRC and UD clones were shipped to the FHCRC core genomics lab. Information on the libraries joined to produce this collection is available at individual web sites and previous publications. Microarrays were constructed using modified protocols of those discussed by De Risi et al. Individual PCR products were verified as unique via gel electrophoresis and purified using the Millipore Multiscreen-PCR filtration system. Purified PCR products were mechanically "spotted" in 3X SSC (1X = 150 mM sodium chloride, 15 mM sodium citrate, pH 7.0) onto poly-lysine coated microscope slides using a GeneMachines OmniGrid high-precision robotic gridder (Genomics Solutions, Ann Arbor, MI). The array layout consists of 32 blocks in a 4 × 8 configuration and each PCR product is represented once on the array. In addition, each array sub-grid (i.e., "block") contains spots representing 4 different Arabidopsis genes (negative controls) and 1 spot consisting of sheared chicken (white leghorn) genomic DNA.