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It is very important to develop the precise tools for designing the siRNAs to get the most efficient knockdown of the target genes and to reduce any off-target effects.
After 6 days of infection, the most efficient knockdown cells, Tat-SF1(B), showed an inability to produce reverse transcriptase above background levels (Figure 3D).
The two hairpins giving the most efficient knockdown are shown.
Similarly, HaCaT cells transduced with construct sh- KEAP1-1 (KEAP1-KD) showed the most efficient knockdown of KEAP1 expression.
4T1 cells with the most efficient knockdown were used for all studies and cultured with gentamicin (50 μg/ml; Calbiochem).
Construct WNT5A-5 had the most efficient knockdown while construct WNT5A-2 caused the greatest inhibition of colony formation.
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Similar to cells cultured under hypoxic conditions, the effects of hStn1 knockdown were greatest in cultures that displayed the most efficient hStn1 knockdown, that is, cells expressing shStn1-2 (Fig. S2A, Supporting information).
Two different shRNA sequences were tested and the one producing most efficient FLNa knockdown was chosen for further analysis.
The clones that were most efficient at gene knockdown were selected for subsequent experiments.
Using explicit integration or the sensitivity analysis, one then could predict the most efficient strategy to knockdown specific features of the system, for example focal complexes or focal adhesions.
Since in our hands the RNAi-mediated protein knockdown was most efficient for the T cell-specific ZAP70 as model gene, activated DO11.10 T cells transfected with ZAP70 specific siRNAs were first functionally analyzed by in vitro restimulation.
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