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Mouse DECIPHER™ shRNA Libraries

Mouse DECIPHER shRNA libraries are pooled, barcoded, lentiviral shRNA libraries optimized for RNAi Genetic Screens in pooled format. They target approximately 10,000 mouse genes.

The DECIPHER RNAi screening platform was an open source project from 2010-2014, created by Cellecta to provide tools for researchers to perform and analyze comprehensive shRNA knockdown screens and to develop a standardized, yet versatile platform for collecting and comparing results from different studies and labs. DECIPHER Project members have published numerous peer-reviewed papers. More information and resources are available on the DECIPHER Project website.

Pooled shRNA Libraries

  • 5 to 6 shRNAs per gene
  • Effective shRNA designs that generate > 70% knockdown for more than 75% of the target genes represented
  • Greater than 90% of the shRNA constructs are present within a 10-fold distribution range
  • Mouse library targets pathway-related and disease-associated mouse genes

Intelligent Barcode Design, Quality Data

  • 18-nt barcodes facilitate Next-Gen Sequencing (NGS) data analysis and identification of functional shRNAs
  • Compatible with Illumina HiSeq, GAIIx, and NextSeq NGS systems
  • Barcodes are identified and converted to lists of genes/shRNA with enumerated barcode data
  • Amplification of shRNA hairpins is not required

The histograms above show the distribution of shRNA/barcode sequences in the DECIPHER plasmid shRNA libraries. Virtually all of the shRNA are present in more than 100 copies and most are around 1,000 copies per 20 million HT sequencing “reads”. Also, there is less than a 10-fold difference between the most and least represented sequences for about 90% of the shRNAs, an indication that the libraries have a balanced representation of all shRNAs.

DECIPHER shRNA Library Specifications

 

Edit
Module Description (click for Gene List) # target mRNAs Sources and Annotations
Mouse Module 1
Signaling Pathway Targets
4,625 KEGG, Reactome, and other expert-curated pathway databases, CSHL Cancer 1000 List, Cancer Genome Atlas, FDA drug targets, MeSH
Mouse Module 2
Disease-Associated Targets
4,520 Same as above

User Manuals

  • DECIPHER™ Pooled Lentiviral shRNA Libraries, v9a (PDF)
  • Pooled Lentiviral shRNA Library Screening Reference Manual, v2a (PDF)

Product Analysis Certificates (PACs)

Product Analysis Certificates are provided as PDF files and are available for download on the Product Manuals and Certificates page in the Resources section.

Cellecta performed an RNAi screen with a DECIPHER library to identify prostate cancer-specific gene targets with therapeutic potential in prostate neoplasia treatment. A viability screen was performed on a set of model prostate carcinoma cell lines.

Click here for the screening data.

Citations from the DECIPHER Project

Next-Gen Sequencing of Samples from Genetic Screens

Cellecta DECIPHER shRNA libraries are provided with a complete protocol and all sequencing information to enable researchers to perform high throughput genetics screens and analysis. However, we do also provide Next-Gen Sequencing (NGS) and analysis services for researchers running their own screens with our libraries. Just provide harvested cells for each time point or treatment condition (one sample), and we extract DNA, amplify, sequence, and assemble the data with some basic analysis.

You provide Cellecta with frozen cell pellets or tissue after screening…

…and Cellecta does the rest:

  • Extracts genomic DNA
  • Amplifies barcodes
  • Performs NGS on the Illumina NextSeq or HiSeq
  • Enumerates shRNA counts from raw sequencing data

Please see the Next-Gen Sequencing and Analysis web page for additional information and how to order.

Available Formats

 

Plasmid DNA Library:

Catalog #Item DescriptionAmount
DHPAC-M1-PDECIPHER Human Module 1, Pathway Targets 200 μg
DHDAC-M2-PDECIPHER Human Module 2, Disease Targets200 μg
DHCSC-M3-PDECIPHER Human Module 3, Cell Surface, Extracellular, DNA Binding Targets200 μg
DMPAC-M1V2-PDECIPHER Mouse Module 1, Pathway Targets200 μg
DMDAC-M2V2-PDECIPHER Mouse Module 2, Disease Targets (plasmid)200 μg

 

Packaged Viral Library:

Catalog #Item DescriptionAmount Provided
DHPAC-M1-V8DECIPHER Human Module 1, Pathway Targets2 x 108 TU
DHDAC-M2-V8DECIPHER Human Module 2, Disease Targets2 x 108 TU
DHCSC-M3-V8DECIPHER Human Module 3, Cell Surface, Extracellular, DNA Binding Targets2 x 108 TU
DMPAC-M1V2-V8DECIPHER Mouse Module 1, Pathway Targets2 x 108 TU
DMDAC-M2V2-V8DECIPHER Mouse Module 2, Disease Targets2 x 108 TU
DHPAC-M1-V9DECIPHER Human Module 1, Pathway Targets1 x 109 TU
DHDAC-M2-V9DECIPHER Human Module 2, Disease Targets1 x 109 TU
DHCSC-M3-V9DECIPHER Human Module 3, Cell Surface, Extracellular, DNA Binding Targets1 x 109 TU
DMPAC-M1V2-V9DECIPHER Mouse Module 1, Pathway Targets1 x 109 TU
DMDAC-M2V2-V9DECIPHER Mouse Module 2, Disease Targets1 x 109 TU

 

What you will receive in addition to your order:

  • Plasmid orders include 10 μg empty library vector, for cloning individual constructs used to validate hits from your screen
  • Virus orders include an additional small aliquot of virus to be used for titering in your target cells

Related Products:

Catalog #Item DescriptionPrice
CPCP-K2AReady-to-Use Lentiviral Packaging Plasmid Mix, 250 μg
(for 25 10-cm plates)
$325
LFVC1LentiFuge™ Viral Concentration Reagent, 1 ml
(for a total of 1 liter supernatant)
$325

Please email sales@cellecta.com for questions or to obtain a quote.