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Mendez et al (2009) showed good correlation between qRT PCR data and microarray findings for SERPINE1, with a correlation coefficient of 0.74.
QPCR confirmed the directionality of the microarray findings for nine out of the twelve genes tested (75%).
Quantitative real-time-PCR confirmed microarray findings for miR-1183 and miR-1299 in both tissue and plasma.
The fold change for most CrWRKYs with a significant response to MeJA was 2 fold or less, similar to our microarray findings for jasmonate responsive Arabidopsis WRKYs (Additional file 3: Table S3).
The microarray findings for MMP1, COL1A1, COL1A2 and CCN2 were independently confirmed by quantitative real-time RT-PCR, showing that MMP1 gene expression was significantly up-regulated while COL1A1, COL1A2 and CCN2 mRNA levels were significantly decreased in fibroblasts that were co-cultured with tumour cells.
Expression of five of those genes was measured using RT-qPCR (Additional file 2: Figure S2), and the results for each gene were consistent with the microarray findings for the effect of 4× and day of lactation on mammary gene expression.
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The microarray findings were independently corroborated for a random set of 14 mRNAs by RT-PCR analysis.
To better utilize the findings derived from gene-expression studies of sepsis, a uniform standard of reporting published microarray findings, such as those required for cancer studies [ 6], should be considered by all study authors in the future.
To confirm and extend the microarray findings, six genes were analyzed for expression changes in Colo205, C6 and HT1080 tumors treated with aflibercept for 8, 24 and 72 h by TaqMan, using primer pairs specific for murine mRNA.
Extracted RNA will be aliquoted into three tubes - one for Agilent RNA quality assessment, one for the transcriptomic microarray, and one for validation of microarray findings by real time polymerase chain reaction.
We have demonstrated an informative approach by combining microarray findings that identified a biological determinant for ECS (SERPINE1) with a promising immunohistochemical marker of adverse outcome (SMA) to identify patients with poor survival in OSCC.
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