Microarray hybridization experiments using a tomato gene chip hybridized with potato RNA allowed the identification of known as well as novel genes that were differentially expressed during tuber cold storage in a single potato genotype.
All the S. pneumoniae study isolates were hybridized once against the TIGR4 reference strain and the microarray hybridization experiments were repeated for isolates which gave poor hybridization results.
Microarray hybridization experiments were performed by NimbleGen Systems using a duplicated dye-swap design.
In fact we might have missed those interesting homeobox genes if we had not performed both the SM RT-PCR and DNA microarray hybridization experiments.
In order to determine the genome-wide gene expression, the same cDNA preparations that were used for SM RT-PCR were also employed in microarray hybridization experiments.
Similarly, we extracted the fluorescence intensity of the corresponding genes from the DNA microarray hybridization experiments and calculated the log2 values.
Finally, the results obtained by qRT-PCR validate our microarray hybridization experiments, which were carried out with bacterial RNA extracted from three independent experiments.
We are also indebted to Kang Liu for assistance in DNA microarray hybridization experiments using the Illumina's Sentrix Human-6 Expression BeadChips.
In order to increase the reliability of the biological validation, the real time RT-PCR was performed on RNA samples originating from a separate set of animals distinct from the ones used for the microarray hybridization experiments.
Together with the two-dozen homeobox genes including those ten described above, we also selected two-dozen genes that exhibited frequent downregulation in the DNA microarray hybridization experiments and determined their gene expression in the clinical breast cancer specimens.
For transcriptional profiling, we followed a cyclic, two-color design and performed 28 oligonucleotide microarray hybridization experiments representing technical and biological replicates of the four cell states under investigation: WT grown in vitro (WT-vitro), WT grown in vivo (WT-vivo), AP grown in vitro (AP-vitro), and AP grown in vivo (AP-vivo), Fig. 1.
