Chang Lab:Notebook/CBE/08/152

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Project Title: Design of whole-genome tiling microarrays for Staphylococcus Aureus and Pseudomonas aeruginosa
DNA microarrays are an established technology for measuring gene expression levels. Recent development of whole-genome tiling microarrays has enabled us to study chromatin-immunoprecipitation-chip, comparative genome hybridization, and genome resequencing. Literature review on general microarray technology, whole-genome tiling microarrays, and tiling microarray design algorithms will be conducted. These algorithms will be applied to design whole-genome tiling microarrays for Staphylococcus Aureus and Pseudomonas aeruginosa.

Expression arrays for PA01 and SA NCTC8325
Expression arrays for the bacterium are completed and can be accessed in the 'FYP' folder in eArray.

Whole genome tiling arrays for PA01 and SA NCTC8325
Simple tiling probes need to be created under Expression application. Then, a BLAST search of the simple tiling probes against the bacteria genome can be conducted to replace the Masking option that is not included while using Simple tiling option. Finally, these probes can then be used for the creation of the whole genome tiling array.

Blasting of probes is done using an external program named CLC genomics workbench 2