Details of the microarray design and hybridization data have been deposited at the NCBI GEO repository with accession number GSE55327.
We describe detailed protocols and results with an integrated platform for studying relative transcript expression, including microarray design and fabrication, analysis and calibration algorithms, and high throughput quantitative real-time PCR.
There are several important considerations regarding microarray design and analysis.
Microarray design and experimentation analysis may be obtained from our recently published manuscript (Kortenhorst et al., 2008).
All primers used in QRT-PCR are shown in Table 2. Microarray design and constructions were carried out as our previous work [28].
Improved versions (v2) of the X. tropicalis genome-wide microarray design and the promoter microarray design are available at the authors' web site (http://www.ncmls.nl/gertjanveenstra).nl/gertjanveenstra
Microarray design and preparation, sample labeling, and microarray hybridization and scanning services were performed by the Harvard Partners Center for Genetics and Genomics (now Partners Center for Personalized Genetic Medicine).
We thank Mike Webster for help with microarray design and Luisa Dougan, Jonathan Adler, Dale Herauf, Michael Ottgen, and Jenna Gravley for synthesis and quality control of microarray chips.
However, this study varied in its experimental approach (e.g., use of one antibody, microarray design and data analysis parameters) and the reported enrichment analysis was based on a comparison between the presence of the CACGTG motif and all other E-box variants grouped together as CANNTG.
Microarray design and hybridization.
Microarray design and analysis have been previously described [ 27, 38].
