Adomas et al. BMC Genomics 2010, 11:477 http://www.biomedcentral.com/1471-2164/11/477 Page 7 of 16 Figure 3 Genes significantly differentially expressed (P ≤ 0.05) by S. cerevisiae growing in nitrogen-poor (light colored bar) and nitrogen-rich (dark colored bar) conditions coding for enzymes involved in urea cycle and metabolism of amino groups; identified by microarray using multi-targeted primers (red) or oligo(dT) primers (blue). The results were validated using RNA sequencing on Illumina platform (grey; bars in the same order as for microarray profiling). Error bars represent 95% credible intervals. NS - statistically insignificant difference (P > 0.05); * or lack of a symbol - significant difference (P ≤ 0.05); † - not well measured. Furthermore, of those nine, five are considered dubious ORFs anyway (see Additional File 4). Quantitative RT PCR validation of microarray profiling and tag sequencing of yeast grown in nitrogen-poor conditions To validate results of microarray and RNA sequencing using MTP, quantitative reverse transcription PCR (qRT-PCR) was performed (Table 5). Five genes were selected that were well measured by the microarray- MTP dataset but that did not produce enough signal in the microarray-oligo-dT dataset to be measured, and that showed the largest differences in expression between samples. In all five of these genes, differential expression in the direction predicted by the microarray- MTP dataset and the RNA-seq dataset was validated. Five genes were also selected that showed the largest, statistically significant differences in the dataset of microarrays primed with MTPs, but that due to lower power showed no statistically significant difference in the dataset of microarrays primed using oligo-dT. In four of these five genes, differential expression in the direction predicted by the microarray-MTP dataset and the RNAseq dataset was confirmed. In the one excep- tion, the qRT-PCR result contradicts the directional trend of all four previous measurements (microarray- MTP, microarray-oligo-dT, RNAseq-MTP, and RNAseq- oligo-dT). Genes that were well measured in both array experiments but that were statistically significant due to the increased power of the MTP-based profiling had gen- erally exhibited fairly low fold changes. Similarly low dif- ferences in expression in the same direction were detected by qRT-PCR, confirming the validity of MTP approach. Microarray mRNA profiling of Neurospora crassa undergoing sexual development The MTP for the N. crassa was designed targeting 9846 protein-coding ORFs. Sequence VWNVNNBDKGGC