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Probing microarray assays in the presence of a hybridization mix retrieves precious information on hybridization kinetics.
Most recently, a total of 12 Cd-responsive miRNAs predicted previously were validated using microarray assays in rice [ 15].
To identify the intrinsic factors that are involved in the neural differentiation of pluripotent stem cells, we performed microarray assays in mouse ESCs undergoing neural differentiation.
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Since pre-amplification was not used in microarray assays, miRNA expression levels in microarray were compared to those in miRNA TaqMan Array A without pre-amplification; 84 miRNAs were detected in both microarray and qPCR-array (Ct ≤ 35).
In conclusion, this study indicates that DNA microarray assays can be reproduced in at least two different facilities, which is a pre-requisite for the development of standard guidelines.
For example, both lncRNA and mRNA of ADAMTS15 were down-regulated in microarray assays; however, the lncRNA was down- but the mRNA was up-regulated in RT-qPCR.
Microarray assays could be informative in this regard.
This time series experiment was repeated with the wild type and a soxR deletion strain, resulting in 18 microarray assays from the three time course experiments (two sets for wild type and one set for ΔsoxR).
Supporting this, we found cadherin1/E-cadherin/CDH1 to be dramatically up-regulated by pRb in our microarray assays, with an average fold-induction of 11.83 over pRb-null cells (P = 0.000, validated by qRT-PCR).
We showed that pRb-deficient cells have significantly reduced expression of OB-cadherin, which appeared among the transcripts that are up-regulated by pRb in our microarray assays, with an average fold-induction by pRb of 4.45 (P = 0.000).
Furthermore, in most microarray assays, a 17% deviation from the true value is not considered large.
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