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In all cases, the quantitative RT-PCR validation indicated that differential expression detected by microarray experiment was highly reliable.
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Analysis of data obtained by microarray experiments was carried out by means of hierarchical gene clustering [ 18] using Cluster 3.0 (open source 2006) and TreeView (Stanford University Labs) software.
Even though the fold changes seen by microarray experiments is typically modest, such experiments may underestimate actual changes in malignant epithelial cells due to the dilution of changes in malignant epithelial cells by stromal cells that constitute a significant proportion of pathological specimens.
The difficulty of interpreting the lists of significant genes produced by microarray experiments is a major challenge.
Results obtained by microarray experiments were validated by quantitative RT-PCR for some selected deregulated genes (CDH11, TFF3, C FAM5C, IL6R, KCMNA1) (data not shown).
High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored data type currently used in translational studies.
High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies.
The results obtained by microarray experiments were verified by real-time quantitative PCR (qPCR) by using the LightCycler 2.0 instrument and LightCycler® FastStart DNA MasterPLUS SYBR Green I (Roche Diagnostics GmbH, Manheim, Germany) as previously described [ 77].
The trends in the expression of these miRNAs detected by microarray experiments were consistent (7 miRNAs) or partially (5 miRNAs) consistent with those determined in stem-loop qRT-PCR analyses.
Accordingly, the results can be divided into three categories: (i) Differential expression in C. glutamicum IB2103 of the 24 genes initially identified by the DNA microarray experiment was confirmed by the RT-PCR approach.
Finally, to study the global changes in gene expression by HIPPI in cell, microarray experiment was carried out.
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