Escherichia coli MG1655 whole-genome tiling microarray design and validation

This research focuses on the design, manufacturing and validation of a new E. coli whole-genome tiling micraorray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The E. coli MG1655 genome is re-acquired with next-generation sequencing and then used to design the tiling microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting E. coli under various growth conditions and then using the tiling microarrays to verify expected gene expression patterns. E. coli MG1655 was grown under 10 different conditions, including a standard condition and 9 stress condidtions. 2 replications were measured for each condition. 2 of the 20 resulted samples were lost due to large bubbles on the microarray surface, and are not included in this series.