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Such false discovery could have been avoided if an independent validation of the microarray findings by a second method, such as bisulfite-pyrosequencing, had been undertaken.
We validated accuracy of the microarray findings by performing qPCR on 12 genes identified as CORT-dependent in the microarray analysis (6 genes activated and 6 genes repressed).
We validated the microarray findings by quantifying irg1, ifit3, and socs3 transcripts via quantitative reverse transcription PCR (qRT-PCR) using several of the original RNA samples as templates.
Downregulation of SLC22A1 mRNA expression in primary human HCC is in line with previously published microarray findings by Park et al., where SLC22A1 showed a significantly reduced expression in HCC [ 17].
Technical validation of the microarray findings by qRT PCR showed a moderately positive correlation between the two methods for SERPINE1 expression (r=0.56, P=0.77), but a poorer correlation for HEXIM1 (r=0.22, P=0.15).
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.
Similar(54)
We confirmed our microarrays findings by Real time PCR on selected genes such as IL-1β IL6, IL-8, MCP3, RANTES and SPHK1, utilizing an aliquot of the same RNA sample that was used for the microarray experiments.
The differing origins can be distinguished by examining specific cytokeratins, and the microarray findings were confirmed by performing immunohistochemistry on paraffin material from the parent tumours.
Key microarray findings were verified by real-time PCR and additional in vitro experiments of matrix synthesis and signal transduction.
Microarray findings were confirmed by real-time reverse-transcription PCR (RT-PCR) using the average value of mRNA from dox untreated SW780-shPSCA samples as calibrator.
HELP microarray data has been submitted to the GEO database for public access (accession number pending) Validation of HELP microarray findings was carried out by MALDI-TOF mass spectrometry using EpiTyper by MassArray (Sequenom, CA) on bisulfite-converted DNA as previously described[31].
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