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To validate the knock-down efficiency of reagents designed by NEXT-RNAi, we designed two independent long dsRNAs for all 49 protein- and lipid-phosphatases expressed in Drosophila D.Mel-2 cells (GEO accession GSE21283).

Designs were calculated for FlyBase release 5.16 using the following settings:

  • Avoid perfect homology equal or higher than 19 nt to any unintended targets
  • Avoid CAN repeats or other low-complexity regions
  • Avoid targeting of 3'-UTRs
  • Avoid significant homology (E-value < 1e-10) of the long dsRNA to any other target
  • Optimal efficiency (using the weighted method)
  • Desired long dsRNA length: 150-175 nt

The complete evaluation report (for FlyBase release 5.24) is available here.


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