Arrayed shRNA Libraries
shERWOOD-UltramiR™ Arrayed shRNA Libraries
- Enabling single-target or combinatorial vector-based genetic RNAi screens at scale in arrayed format
- shRNAs designed by shERWOOD algorithm – read the publication in Molecular Cell
- UltramiR microRNA scaffold increases shRNA processing and potency
- Highly efficient retroviral and lentiviral vector backbones for producing high-titer retroviral or lentiviral particles
- Exceptionally bright ZsGreen fluorescent reporter
- All shRNA constructs are 100% sequence-confirmed
- Order premade or custom arrayed shRNA Libraries
shERWOOD-UltramiR arrayed shRNA Libraries allow single-target or combinatorial genetic screens to be carried out at scale in a multiplexed or arrayed format. shRNAs are designed using the shERWOOD algorithm to optimize knockdown efficiency and was developed and validated in Dr. Gregory Hannon’s laboratory at Cold Spring Harbor Laboratory (Knott et al 2014). It is based on the functional testing of over 250,000 shRNA sequences using a high-throughput sensor assay and uses key sequence characteristics for predicting shRNA potency to select the rare shRNA designs that are potent at single copy representation in the genome. Moreover the library uses an alternate microRNA scaffold called “UltramiR“. The UltramiR scaffold has been optimized for increased shRNA processing and potency based on the key determinants for primary microRNA processing (Auyeung et al 2013).
Human and Mouse Whole Genome shERWOOD-UltramiR™ Arrayed shRNA Libraries
The shERWOOD-UltramiR™ Arrayed shRNA Libraries in the retroviral vector pLMN-ZsGreen-Neomycin, covering the Human and the Mouse Genome were developed by transOMIC in partnership with Cold Spring Harbor Laboratory The shERWOOD algorithm combined with the UltramiR backbone were used to design and construct human and mouse genome-wide, sequence-verified, arrayed shRNA libraries featuring superior knockdown efficiencies:
Construction and Validation of an shRNA-Specific Predictive Algorithm (hhERWOOD) (A) Consolidated cross-validation of predictions versus sensor scores for all shRNAs in the Fellmann et al. (2011) data set (shRNAs are separated by the guide 5 0 nucleotide). (B) GO term instances associated with the targeted gene set selected for shRNA validation screens. (C) GO term instances associated with genes for which at least two hairpins were significantly depleted in each of the TRC, Hannon-Elledge (HE), and shERWOOD (SW) validation screens. (D) The percentage of shRNAs targeting consensus-essential genes that were depleted in each of the TRC, HE, and shERWOOD shRNA screens. The plot was made with the Matlab Boxplot function using default parameters. The edges of the box are the 25 th and 75 th percentiles. The error bars extend to the values q3 + w(q3 ? q1) and q1 ? w(q3 ? q1), where w is 1.5 and q1 and q3 are the 25 th and 75 th percentiles. (E) Average log-fold change for shRNAs targeting consensus-essential genes (per gene) for each of the TRC, EH, and shERWOOD validation screens. The plot was made with the Matlab Boxplot function using default parameters. The edges of the box are the 25 th and 75 th percentiles. The error bars extend to the values q3 + w(q3 ? q1) and q1 ? w(q3 ? q1), where w is 1.5 and q1 and q3 are the 25 th and 75 th percentiles. (F) The percentage of shRNAs corresponding to consensus-essential genes that, for any given shERWOOD score, were depleted in the shERWOOD validation screen.
You can purchase the human and mouse whole genome wide arrayed dual sgRNA libraries (Gene List downloads: Human Mouse) or you can pick and choose for building a custom arrayed library.
Retroviral shRNA vector pLMN-ZsGreen-Neomycin
Custom Arrayed shRNA Libraries at any size
Our partner transOMIC Technologies offers maximal flexibility for your arrayed shRNA screening project, based on their wealth of vectorology, and clone handling experience:
pZIP Constitutive shRNA Lentiviral Vector Options
pZIP-TRE3G Inducible shRNA Lentiviral Vector Options
pLMN Constitutive shRNA Retroviral Vector
pLMP-d Constitutive shRNA Retroviral Vector
- Build your custom shRNA array cloned in any of transOMIC´s lentiviral or retroviral vectors for shRNA expression. If you prefer your own lentiviral vector, we can accomodate this, too!
- shRNAs for your target gene list will be designed using the shERWOOD algorithm or you can share your own shRNA designs
- Oligos are synthesized and cloned into your choice of lentiviral or retroviral vector.
- Each clone is sequence-verified and arrayed into 96-well plates.
- We can deliver glycerol stocks, plasmid DNA, and/or ready-to-use lentiviral particles in 96-well plates.
Please contact us with your project details and share your gene list, the number of shRNAs needed for targeting each gene, and your vector choice with us. We will be pleased to send you a detailed quotation.