siRNAnormally arrayed in 96-well or 384-well plates can combine multiple siRNAs targeting different sequences in the same gene in one well (SMARTPools) can be purchased in “ready-to-transfect” aliquots or in larger amounts that require replating can also be arrayed on slides | Consistent quality of reagents Ease of use and readily transfectable Chemical modification of siRNA can limit off-target effects | Finite resource Target cells need to be transfectable Relatively short period of silencing Not suited to pooling strategies |
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shRNA as:plasmid DNA arrayed in 96-well or 384-well plates for transfection viral particles in multi-well plates (one shRNA per well) pools of plasmids or viral particles | Renewable resource Viral vectors enable silencing in difficult-to-transfect cells Suited to pooled screens as well as arrayed screens Stable integration of silencing machinery into host cell genome enables longer-term silencing Varying vector formats available that allow inducible silencing, tracking of silencing machinery, etc | Reduced ease of use: require preparation of plasmid DNA and, in the case of viral-based libraries, viral packaging Viral use often requires biological containment Pooled screens require significant deconvolution |