Design of whole-genome tiling microarrays for pseudomonas aeruginosa PAO1.

• Main Author: Chong, Anna Siew Chyn.
• Other Authors: Chang Wook, Matthew
• Format: Final Year Project
• Language: English
• Published: 2010
• Subjects: DRNTU::Engineering::Chemical engineering::Biotechnology
• Online Access: http://hdl.handle.net/10356/39477
• Institution: Nanyang Technological University

Whole-genome tiling microarrays (WGTAs) are an established tool for the characterization of complete genome. This technology is of paramount important in the microbiology industry due to its recent development in the various applications [1]. However, most of the probe design for microarrays is unsatisfactorily selective. Hence, it is vital to design optimal probes in order to enhance the validity of microarrays. This report presents an extensive literature review on the microarrays technology and its design algorithms. A design plan for the WGTAs using Agilent eArray was described, including discussions of the design strategy and challenges encountered. Results show that a total of 62,561 60-mer PAO1 probes were created via Agilent eArray and optimized by CLC bio Basic Local Alignment Search Tool (BLAST). These optimal probes were used to design the WGTAs for chromatin immunoprecipitation (ChIP) and comparative genome hybridization (CGH) applications using Agilent eArray. Further enhancements can be done on the design methodology, which include refining the probe selection criteria and other influential parameters, reducing the probes spacing to improve the genome coverage, performing a BLAST search of PAO1 probes against other strains, and validating the quality of WGTAs through experiments.