Table 1 RNAi library formats
Library typeAdvantagesDisadvantages
  • normally 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

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