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Exact(7)
The choice of candidate genes was based on the statistical significance obtained following an ANOVA test of the microarray results (see results section).
The qPCR results confirmed the microarray results (see Supplemental Material, Table S2).
Expression profiles were validated for all selected genes and for both organs, showing that qPCR results are in complete accordance with microarray results (see Additional file 2).
At other stages some of the RT-PCR results although not significant do showed a trend that resembled the microarray results (see actin 3 at 3-dpe).
However, comparison of microarray results (see Additional file 3:_List of differentially expressed genes) with qPCR data (Fig. 4) indicated that in this respect, our microarray setup is more likely to pick up slightly divergent sequences than the gene expression "gold standard" qPCR.
Zebrafish CYP11A2 is 80% identical to CYP11A1 at the amino acid level, but little is known about functional similarities between the two forms, or about CYP11A2 expression, although based on our microarray results (see below) it appears to be expressed in the early embryo, and database EST evidence indicates that it is also expressed in adult gonads.
Similar(53)
NO-induced changes in transcript abundance as determined by microarray were consistent with these results (see Additional file 3, part B]. Real-time RT- PCR (TaqMan®) was used to validate NO-mediated changes in mRNA levels (Fig. 2A and 2B).
The time point 300 min of the kinetic of Cd responses was repeated twice (independent biological repeats, columns 300 and 300') with the two different versions of the Cyanochip DNA microarrays, leading to very reproducible results (see Additional files 2 and 4).
This normalisation appeared to be more suitable than RUV [ 20] and SVA [ 21] improving concordance with microarray results as seen in Additional Figures 1 and 2 in Additional File 1. Sample variances from three datasets were used as sources of additional information to aid in the estimation of the common variance.
Ensuing microarray gene expression analysis supported these reporter assay results (see below).
Consistent with other reports [ 35, 36], the microarray ratios were compressed compared to qRT-PCR results (see Additional file 3).
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