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The time point for maximum target gene suppression generally varies depending on the number of miRNA binding sites at the 3′ UTR of the target gene and the extent of complementarity of the seed region [ 37].
ON-TARGET plus siRNA (Dharmacon, Lafayette, CO, USA) smart pool is a mixture of four siRNAs targeting AQP3, which attains the maximum target gene silencing and reduces the overall number of off-target interactions.
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The position of location where the fluorescent intensity was maximum of each target gene and the amplification ratio were plotted as a function of time during the ICP operation.
The maximum reduction of each target gene varied from 50% to 82%.
Here, M max is a prior restriction on the maximum number of TFs per target gene; in this study M max = 4.
The amplification of genomic DNA typically amounted to a maximum of <1% of the target gene when extracting RNA by TRIzol [ 37].
However, this problem is NP-hard [we used the distinguishing substring selection problem (DSSP) [ 47, 48] to prove that finding a qualified siRNA that has the maximum number of target genes is NP-complete, and the proof is presented in Additional file 2.
Importantly, in 4 of those cases the maximum MDP score was at the target gene itself and in the remaining 7 cases it was very close (<500 kb) to the target gene.
The amplification of genomic DNA typically amounted to a maximum of <1% of the target gene when using the TRIzol protocol and even less when using RNeasy columns including DNase-treatment.
Recall that r is the maximum order of regulation between the target gene and its regulators.
In this test, we collected the maximum absolute expression change observed for each target gene when genes co-localized with eQTL in the 99 th percentile are mutated.
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