ORF Microarrays and Gene Expression Profiling

We have built an array containing probes for all the known and predicted open reading frames (ORFs) of the fission yeast genome. For each ORF, exon sequence is amplified by PCR using gene-specific primer pairs. A second round of PCR is performed with a universal forward primer containing a 5'-aminolink and the gene-specific reverse primers. The coding strand of each probe can then be covalently linked to glass slides via the 5' amino group. Whenever possible, primers and amplicons were selected from regions that did not show close homology to other regions in the fission yeast genome. The array also contains 'pseudogenes', all mitochondrial ORFs, several introns and various control spots. We are printing all elements in duplicate as an internal control for reproducibility (total ~13,000 array elements).

• For details on our microarray design see:
  Lyne R, Burns G, Mata J, Penkett CJ, Rustici G, Chen D, Langford C, Vetrie D, and Bähler J (2003). Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data.
  BMC Genomics 4:27 (PDF).

• Primer sequences for the ORF array are available here: Primer information
  

• Searchable database of primer sequences, parameters, mappings, and amplicons for both the intragenic (ORF) and intergenic arrays:

  Search for Intragenic Primer by ID:

  Include Wildcards: Yes No

  Search for Intergenic Primer by ID:

  Include Wildcards: Yes No

• This searchable primer database has been described in:
  Penkett CJ, Birtle ZE, and Bähler J (2006). Simplified primer design for PCR-based gene targeting and microarray primer database: two web tools for fission yeast.
  Yeast 23:921-928 (PDF).