AAV shRNA Library
AAV shRNA Library
An AAV-shRNA library is a powerful pooled screening tool that uses adeno-associated virus (AAV) to deliver large collections of short hairpin RNAs (shRNAs) into cells, tissues, and whole organisms. Each shRNA in the library targets a specific gene for knockdown through RNA interference (RNAi), enabling high-throughput identification of gene functions, regulators, and therapeutic targets.
Compared to lentiviral shRNA libraries, AAV-shRNA libraries offer unique advantages—stable expression in non-dividing cells, broad tropism, low toxicity, long-term in vivo expression, and compatibility with tissue-specific AAV capsids. This makes them especially suited for CNS, muscle, liver, immune system, and organoid-based functional genomics, as well as in vivo pooled screening in mice and non-human primates.
AAV-shRNA libraries are typically delivered as a pooled viral population, maintaining high diversity (10⁴–10⁶ shRNAs or more). Each shRNA can be tracked using next-generation sequencing, enabling researchers to measure enrichment or depletion of specific guides after selection.
Applications
- Genome-wide and targeted loss-of-function screening
- Pathway discovery and modifier identification
- Synthetic lethality studies
- Target validation for drug development
- In vivo pooled CRISPR/RNAi screening
- Organoid-based functional genomics
End-to-End Library Services
AAVnerGene manages every step of the workflow:
Library design & shRNA selection
High-coverage cloning and amplification
NGS diversity confirmation (optional)
AAV packaging at 10¹²–10¹⁴ vg scale
Quality control: titer, purity, full/empty ratio, and infectivity
Follow-up evolution or screening support
AAV-shRNA Library Design
At AAVnerGene, we offer two flexible and scalable approaches to design your AAV-shRNA library—whether you prefer to use an existing validated shRNA collection or build a fully customized library from scratch. Our goal is to ensure optimal diversity, balanced representation, and high functional performance for your screening applications.
| Feature | From Existing shRNA Collections | Fully Custom AAV-shRNA Library Design |
|---|---|---|
| Source of shRNAs | Pre-validated, published, or commercially available shRNA sets | Entirely custom-designed based on your target genes |
| Design Flexibility | Limited to sequences already available | Full control over target genes, number of shRNAs/gene, targeting region, GC content, off-target filtering |
| Complexity | Usually fixed based on the existing library (10³–10⁵) | Flexible—small focused libraries to large genome-wide screens (10²–10⁶+) |
| Turnaround Time | Fastest option; minimal design effort | Longer design and validation phase |
| Cost | Lower, due to no sequence design work | Higher, due to custom sequence design and synthesis |
| Performance Validation | Often includes prior functional data | Can incorporate computational scoring (on-target/off-target) and optimized RNAi rules |
| Applications | Standard pathway studies, well-known gene sets | Novel target discovery, unique gene panels, species-specific targets |
| Sequence Optimization | Limited | Fully optimized for structure, stability, and knockdown efficiency |
| Barcode Integration | Optional | Fully customizable barcoding strategy (1–10+ barcodes/shRNA) |
| Species Compatibility | Based on available collections | Designed for any species (human, mouse, rat, NHP, etc.) |
| Best For | Fast, cost-effective studies using known genes | High-precision, tailored functional genomics or novel discovery projects |
shRNA oligo pool
Oligo Pools Pricing at AAVnerGene
Complexity | 20 – 120nt | 121 – 150nt | 151 – 200nt | 201 – 250nt | 251 – 300nt |
| 2-100 Oligos | $400.00 | $480.00 | $540.00 | $700.00 | $1,000.00 |
| 101-500 Oligos | $800.00 | $960.00 | $1,080.00 | $1,400.00 | $2,000.00 |
| 501-1,000 Oligos | $1,200.00 | $1,440.00 | $1,620.00 | $2,100.00 | $3,000.00 |
| 1,001-2,000 Oligos | $1,600.00 | $1,920.00 | $2,160.00 | $2,800.00 | $4,000.00 |
| 2,001-6,000 Oligos | $2,400.00 | $2,880.00 | $3,240.00 | $4,200.00 | $6,000.00 |
| 6,001-12,000 Oligos | $3,200.00 | $3,840.00 | $4,320.00 | $5,600.00 | $8,000.00 |
| 12,001-18,000 Oligos | $4,000.00 | $4,960.00 | $5,400.00 | $6,800.00 | $10,000.00 |
| 18,001-24,000 Oligos | $5,200.00 | $6,400.00 | $7,200.00 | $8,800.00 | $13,000.00 |
| 24,001-30,000 Oligos | $6,800.00 | $8,400.00 | $9,000.00 | $11,800.00 | $16,400.00 |
| 30,001-42,000 Oligos | $7,800.00 | $9,600.00 | $11,600.00 | $13,000.00 | $20,000.00 |
| 42,001-54,000 Oligos | $9,400.00 | $11,800.00 | $13,200.00 | $16,000.00 | $23,000.00 |
| 54,001-72,000 Oligos | $10,800.00 | $13,000.00 | $14,200.00 | $18,000.00 | $27,000.00 |
| 72,001-96,000 Oligos | $11,800.00 | $14,000.00 | $15,000.00 | $19,000.00 | $29,000.00 |
| 96,001-120,000 Oligos | $12,800.00 | $15,000.00 | $16,000.00 | $20,000.00 | $31,000.00 |
| 120,001-150,000 Oligos | $13,800.00 | $16,000.00 | $17,800.00 | $22,000.00 | $33,000.00 |
| 150,001-180,000 Oligos | $14,800.00 | $18,000.00 | $19,200.00 | $24,000.00 | $36,000.00 |
| 180,001-210,000 Oligos | $15,800.00 | $19,200.00 | $21,800.00 | $26,000.00 | $39,000.00 |
| 210,001-240,000 Oligos | $17,200.00 | $21,800.00 | $23,200.00 | $28,000.00 | $43,000.00 |
| 240,001-300,000 Oligos | $21,000.00 | $25,500.00 | $27,000.00 | $33,000.00 | $49,000.00 |
| 300,001-360,000 Oligos | $25,200.00 | $30,600.00 | $32,400.00 | $39,000.00 | $59,000.00 |
| 360,001-420,000 Oligos | $29,200.00 | $36,000.00 | $38,000.00 | $46,000.00 | $70,000.00 |
| 420,001-480,000 Oligos | $33,600.00 | $41,000.00 | $43,200.00 | $52,800.00 | $82,000.00 |
| 480,001-600,000 Oligos | $41,200.00 | $50,000.00 | $53,200.00 | $64,800.00 | $100,000.00 |
| 600,001-696,000 Oligos | $48,800.00 | $60,000.00 | $63,000.00 | $78,000.00 | $114,000.00 |
AAV shRNA Library Construction
| Component | Options | Default Recommended |
|---|---|---|
| shRNA Promoter | U6, H1, tRNA, Pol II (for miRNA based shRNA) | U6 |
| Reporter Promoter | CMV, EF1a, CAG, hSyn….. | CMV |
| Reporter | EGFP, mCherry, Luc, BFP | EGFP |
| AAV Genome | ssAAV or scAAV | ssAAV |
| Production System | AAVone, AAVdual, AAVtri | AAVtri |
| Barcoding | 0–10+ barcodes per shRNA | No |
AAVnerGene offers both traditional single shRNA backbones and miR30-based backbones for flexible and efficient gene silencing.
AAV shRNA library construction can be done using a variety of methods, including restriction enzyme digestion, ligation-independent cloning, or Gibson assembly. Our pricing is dependent on quantity and transfection conditions. Pricing increases with lower copies per cell.
Library complexity | Price | Turnaround Time |
1.00E+07 | $12,800 | 2-3 weeks |
1.00E+08 | $21,800 | 2-3 weeks |
| 1.00E+09 | $68,000 | 3-4 weeks |
| Higher | Please contact us to discuss | |
Note: Complexity is calculated based on the number of clones obtained after transformation. We also provide NGS (Next-Generation Sequencing) services to verify library diversity, available for an additional fee.
AAV shRNA Library Production
Packaging of AAV shRNA Library follows the same process as standard AAV packaging. Please contact us (customer@aavnergene.com) to request a customized quote.
AAV shRNA Library Validation
Validation of the AAV Enhancer Library is conducted using next-generation sequencing (NGS) to quantitatively assess enhancer integrity, diversity, and accurate enhancer-barcode pairing.
AAV shRNA Library Evolution
Library Packaging & Validation
Package the pooled shRNA library into high-quality AAV vectors and confirm diversity with next-generation sequencing (NGS).Initial Infection
Transduce target cells or animal models at low multiplicity of infection (MOI) to ensure predominantly single-vector delivery per cell.Selection Pressure Application
Apply experimental conditions (e.g., drug treatment, stress, or disease modeling) to select for cells harboring functional shRNAs.Sample Collection & DNA Extraction
Harvest cells or tissues exhibiting the phenotype of interest and extract genomic DNA for shRNA sequence recovery.Next-Generation Sequencing (NGS)
Sequence recovered shRNA inserts to quantify guide representation and identify enriched or depleted shRNAs.Data Analysis & Hit Identification
Analyze sequencing data to pinpoint candidate shRNAs driving the phenotype.Iterative Rounds
Repackage enriched shRNA pools for additional selection cycles, enhancing screen sensitivity and specificity.