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To confirm the specific thyroid cell expression of the modulated microRNAs, we performed Laser Captured Microdissection (LCM) on frozen sections from the deep-sequenced samples, and we analyzed the expression profiles of the 20 microRNAs by qRT-PCR in the normal and tumor thyroid cells.
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The mean expressions of the modulated intergenic transcripts were in accordance with those found by the array.
By combining the assembly and integration strategies, we were able to generate strains with a diverse set of genetic designs, where each strain contained a unique combination of promoters driving expression of the four modulated genes (Fig. 2d).
We investigated the expression of the CT highly modulated genes in C berries (Table 4), which allowed us to distinguish between those not expressed in C berries and those expressed but not highly modulated in C berries.
Furthermore, in most published GEP data sets analyzing purified MM or AML cells, the expression of the inducible contact-modulated genes was generally high as opposed to the 'silence' of these genes when recorded during homeostasis (immediately following aspiration).
To confirm the modulated expression of the selected target genes, 20x Assays-On-Demand™ gene expression primers and probes (Applied Biosystems) were used.
To confirm the modulated expression of the selected genes 20× Assays-On-Demand™ gene expression primers and probes (Applied Biosystems) were used.
Although the analysis of the modulated expression of genes did not indicate a significant increase in the expression of transporters (Fig. 3), a survey of the most highly expressed genes indicated that many cellular transport systems are induced in germinating conidia (see Additional file 3).
As PDR12 has been implicated in sorbic acid resistance [ 46], we investigated whether variation of the expression of this gene modulated resistance to this acid.
The expression patterns of the BER modulated strains were compared to our previously published data of the transcriptional response of yeast when exposed to the alkylating agent, methyl methanesulfonate (MMS), at two doses 0.05% and 0.1% [1].
The genome-wide expression levels of the BER modulated strains were compared to wild type yeast and the differentially expressed genes were identified (see Materials and Methods); a total of 633 ORFs were identified with statistically significant changes compared to wild type yeast in at least one condition (Fig. 4, Dataset S1).
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