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The RNAi Consortium

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Title: The RNAi Consortium  
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The RNAi Consortium

The RNAi Consortium, or TRC, is a Sigma-Aldrich and Open Biosystems.


  • Hairpin selection 1
  • Hairpin vector 2
  • Release 3
  • External links 4

Hairpin selection

A set of candidate hairpins are selected based on the 1st Refseq transcript from each NCBI gene. They should be 21mers, be at least 25bp from start of the coding sequence and no closer than 150bp from its end. Candidates are scored based on various empirical rules (see the Broad Institute's web site for a complete list [1]) and then BLASTed against 2 transcriptome sets. Hairpins that are unique for a Unigene cluster and a RefSeq NM identifier are preferred. Lastly, the candidates are spaced to have 1 hairpin in the 3' untranslated region and 4 in the coding sequence.

Hairpin vector

Selected hairpins are cloned into the vector pLKO1, which is a multipurpose plasmid that can be propagated in bacteria, transfected into mammalian cell lines or used for generation of lentiviruses. It contains resistance genes against ampicillin and puromycin.


Release 1 of the TRC lentiviral shRNA libraries consist of about 35'000 shRNA constructs against 5300 human (25'000 clones) and 2200 mouse genes (10'000 clones). Release 2 of the human shRNA library contained an additional 9'500 clones. Releases occur roughly every quarter. The completing of both mouse and human libraries is envisioned for the end of 2006 or beginning of 2007.

External links

  • TRC homepage at the Broad Institute
  • TRC hairpin selection rules
  • Sigma-Aldrich TRC intro page
  • OpenBiosystems TRC intro page
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