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Through the straightforward mixing of two block copolymers, the level of gene knockdown was easily optimized to achieve the maximum level of GAPDH protein silencing in NIH/3T3 cells (~70%) using a single siRNA dose.
For all experiments, we examined the effects of the knockdowns in the R1 mESC line first using two types of siRNA expression plasmid and then confirmed the effects in the E14TG2a line using a single siRNA expression plasmid.
Given the inherent difficulty in controlling for off-target effects in any knockdown experiment performed using a single siRNA, the results presented here should be subjected to independent validation with use of a second siRNA.
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For CENP-C silencing, we used a single siRNA (target sequence: 5′-GGAUCAUCUCAGAAUAGAA-3′ from AMBION, Austin, TX) at a concentration of 7.5 nM.
This cotransfection did not reduce the proportion of S phase cells more than was achieved using either a single siRNA separately (Supplementary Figure S2).
Five hours after transfection with GAPDH-specific siRNA using a single HV pulse, MFI values were only slightly higher than for non-transfected preadipocytes.
Using a single booster.
However, it has been suggested that instead of a single siRNA, using a combination of 2 3 siRNAs targeting multiple genomic regions may be ideal to enhance efficacy and reduce viral escape as well as off-target effects [16].
A single siRNA molecule was used for each positive control gene: KIF11 (siRNA ID #105925), PLK1 (siRNA ID #213548).
(A ) Peanut Agglutinin (PNA) lectin staining quantification after depletion of the 12 Tn regulators with a single siRNA from the pool used in the screen and in COSMC knockout cells.
Viral titers were reduced 80-fold with 37.5 pmol of a single siRNA or with as little as 6.25 pmol of each siRNA when used in combination.
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