short hairpin RNA (shRNA) Design

• The RNAi Consortium shRNA Library    (The RNAi Consortium) - This page provides search tools for short hairpin RNA (shRNA) clones produced by the The RNAi Consortium (TRC), as well as protocols for handling and conducting screens with shRNA molecules. You can also look up the oligonucleotide sequences for the construction of your own shRNA clones for those mouse and human genes where the consortium has yet to produce shRNAs. The algorithm we use to pick shRNA targets attempts to maximize effectiveness in knocking down mRNA transcripts while maintaining target gene specificity.

• Insert Design Tool for the pSilencer™ Vectors  (Ambion) - This tool will generate hairpin siRNA-encoding DNA oligonucleotide insert sequences from an input siRNA target sequence, for cloning into a pSilencer siRNA Expression Vector. The program will add the loop sequence and overhangs for cloning

• shRNA Explorer™  (Genelink) - Genelink shRNA design tool with guidelines, options for loop sequences, length of dsRNA and restriction site

• siRNA Hairpin Oligonucleotide Sequence Designer  (Clontech) - Clontech tool for design shRNA oligos

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