Custom Pooled shRNA Libraries

Cellecta Custom Lentiviral Pooled shRNA Library Service 

There are many technical challenges that need to be overcome to produce shRNA libraries with specific, representative, evenly distributed elements that are amenable to Next-Generation Sequencing (NGS) read-outs.
Our well experienced partner Cellecta offers both, ready-to-use, off-the-shelf genome-wide lentiviral shRNA libraries, as well as custom-designed lentiviral shRNA pooled libraries targeting any set of genes, enabling you to assay the functional effects of many hundreds to many thousands of shRNA constructs in one experiment. Cellecta can produce precisely defined high quality custom pooled lentiviral libraries with well designed shRNAs targeting any set of your genes of interest in about 6 weeks of time.

Custom pooled shRNA lentiviral library service description:

1. shRNA Design 

Our partner Cellecta has pioneered shRNA designs and construction of complex pooled shRNA libraries. You can rely on more than 15 years of experience resulting in many hundreds of successfully used custom shRNA libraries. For citations click here.

Designing effective shRNAs is essential for effective RNAi knockdown screening. In addition to choosing the optimal sequence, there are a number of structural factors that affect shRNA efficacy. In addition, the stem-loop hairpin structure of shRNA poses challenges for library construction and amplification. To create representative quality shRNA libraries, Cellecta have focused significant effort to optimize the shRNA inserts in their libraries and tested shRNA structure variations in a large-scale shRNA efficacy reporter assay. On top of this structure optimization Cellecta have developed an in-house bioinformatics algorithm to predict the most effective shRNA sequences, and combine this with published data of validated sequences when constructing their libraries. For further information about Cellecta´s shRNA library design click here. 

In case you like an shRNA library to be manufactured using already designed shRNA sequences, we can accomodate this as well.

Cellecta delivers shRNA libraries including shRNA-specific barcodes avoiding the tedious sequencing of shRNA hairpin structures.

2. Oligo Pool Synthesis and Cloning

shRNA and barcode sequences are synthesized as a pool on an Agilent oligo synthesis chip ensuring high representation of each oligo in the pool.

A panel of non-targeting, intron-targeting, non-specific, or lethal shRNA controls can be added to the pool according to your requirements to provide reference standards when analyzing screening results.

The shRNA pool can be cloned in a wide variety of Cellecta lentiviral shRNA cloning vectors, enabling either constitutive or inducible shRNA expression.

3. Quality Analysis

Once the library is made, a few dozens of constructs are isolated for full-insert Sanger sequencing to confirm the configuration of the shRNA and barcode expression cassette and ensure correct insertion. The complete library pool is deeply QC- sequenced by NGS to confirm full representation of all shRNAs and assigned barcodes in the pool, and assess their distribution.

4. Deliverables

We provide 500 µg of the plasmid library and the following information:
– Complete sequence information for all shRNAs & assigned barcodes, and the vector chosen by you
– NGS shRNA/barcode distribution data
– Complete cloning site design
– Primer information for sequencing

Please use our Service request form  to contact us for more details or request a quote


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