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It has been demonstrated that antisense RNA amplification not only preserves the fidelity of RNA-based microarray analysis but even improves the sensitivity.
The data suggest that significant differential gene expression can be missed by expression microarray analysis but recaptured by integrating functionally relevant epigenetic modifications such as H3K9 acetylation.
Two phosphodiesterase transcripts, PDE7A and PDE4D, were validated by quantitative PCR and a third, PDE8A was identified by microarray analysis but not validated.
In general, the direction of change in mRNA levels agreed completely with the microarray analysis, but with larger mean fold differences (Figure 3A and Table S2).
Upregulation of both molecules was initially detected in the microarray analysis, but was subsequently confirmed by FACS and real-time RT-PCR respectively.
One explanation could be that these isolates contained novel variants of known tet genes that hybrized with the probes used for miniaturized microarray analysis, but which were not complementary to the PCR primer sets used.
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Significant research efforts have gone into developing microarray analysis techniques, but the field is ripe for research to characterize the variability and errors introduced by the scanning process itself, the scanner instrumentation, and the user.
PANA was developed in the microarray analysis context, but can be extended to other high-throughput methodologies provided that a functional database is available for feature annotation.
The expression ratios are consistent but slightly higher than those determined by microarray analysis [ 34], but not enough to reach the 2.5 fold values established by Paul et al. [ 14].
Single-cell microarray analysis is possible, but technically difficult and highly time-consuming [ 7].
Using microarray analysis, HIF-1α but not HIF-2α has been shown to regulate the levels of glycolytic genes (44).
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