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Biomedicum Genomics Oy
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Genome Scale shRNA Libraries

  The RNAi Consortium (TRC) is a collaborative group of world-renowned academic and corporate life science research groups whose mission is to create comprehensive tools for functional genomics research and make them broadly available to scientists worldwide.

The TRC-1 human and mouse shRNA libraries were developed at the Broad Institute of MIT and Harvard and currently consist of ~159,000 pre-cloned shRNA constructs targeting ~16,000 annotated human genes (TRC-Hs 1.0) and ~15,950 annotated mouse genes (TRC-Mm 1.0) for RNA interference-mediated gene silencing.

TRC shRNA clones, designed and developed by the RNAi Consortium at the Broad Institute of MIT and Harvard, include hairpin sequences comprised of a 21 base stem and a 6 base loop. Rules based design consisting of sequence, specificity, and position scoring were utilized to generate optimal shRNA sequences. The hairpin sequences were each cloned into the pLKO.1 vector and sequence verified. Typically, 3-5 shRNA constructs were created for each target gene to provide varying levels of knockdown and to target different regions of mRNA transcript. Two in five clones will typically provide at least 70 % knockdown of the gene target. Most target sets include an shRNA clone targeting the 3'UTR for use in phenotypic rescue studies using cDNA expression constructs.

shRNA constructs can provide varying levels of knockdown in different systems and cell lines, and therefore BMGen strongly recommends validating the knockdown achieved in your system.

While the TRC shRNA clones were designed to minimise any recombination events, all genome-scale libraries of this nature have inherent errors due to spontaneous mutations occurring during plasmid propagation and purification. For this reason, BMGen offers sequencing of all clones ordered at an affordable price. Please contact us for more information.

Due to the dynamic maintenance procedures of the TRC library held by BMGen, no global error rate has previously been determined for this library. BMGen is currently undertaking sequencing of the library to evaluate the inherent error rate and will make the results available when sequencing has been completed.

miRNA adapted shRNA libraries