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
|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
|4,520||Same as above|
- 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.
Citations from the DECIPHER Project
- Gao M, Monian P, Pan Q, Zhang W, Xiang J, Jiang X. Ferroptosis is an autophagic cell death process. Cell Res. 2016 Aug 12. doi: 10.1038/cr.2016.95. [Epub ahead of print] PubMed PMID: 27514700.
- Li Q, Karim AF, Ding X, Das B, Dobrowolski C, Gibson RM, Quiñones-Mateu ME, Karn J, Rojas RE. Novel high throughput pooled shRNA screening identifies NQO1 as a potential drug target for host directed therapy for tuberculosis. Sci Rep. 2016 Jun 14;6:27566. doi: 10.1038/srep27566. PubMed PMID: 27297123; PubMed Central PMCID: PMC4906352.
- Yeddula N, Xia Y, Ke E, Beumer J, Verma IM. Screening for tumor suppressors: Loss of ephrin receptor A2 cooperates with oncogenic KRas in promoting lung adenocarcinoma. Proc Natl Acad Sci U S A. 2015 Nov 5. pii: 201520110. [Epub ahead of print] PubMed PMID: 26542681.
- Guo J, Liu H, Zheng J. SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. Nucleic Acids Res. 2015 Oct 29. pii: gkv1108. [Epub ahead of print] PubMed PMID: 26516187.
- Kobayashi H, Nishimura H, Matsumoto K, Yoshida M. (2015) Identification of the determinants of 2-deoxyglucose sensitivity in cancer cells by shRNA library screening. Biochem. Biophys. Res. Commun. :null. PMID: 26403972
- Chan SM, Thomas D, Corces-Zimmerman MR, Xavy S, Rastogi S, Hong WJ, Zhao F, Medeiros BC, Tyvoll DA, Majeti R. (2015) Isocitrate dehydrogenase 1 and 2 mutations induce BCL-2 dependence in acute myeloid leukemia Nat. Med. 21(2):178-84. PMID: 25599133
- Lin L, Sabnis AJ, Chan E, Olivas V, Cade L, Pazarentzos E, Asthana S, Neel D, Yan JJ, Lu X, Pham L, Wang MM, Karachaliou N, Cao MG, Manzano JL, Ramirez JL, Torres JM, Buttitta F, Rudin CM, Collisson EA, Algazi A, Robinson E, Osman I, Muñoz-Couselo E, Cortes J, Frederick DT, Cooper ZA, McMahon M, Marchetti A, Rosell R, Flaherty KT, Wargo JA, Bivona TG. (2015) The Hippo effector YAP promotes resistance to RAF- and MEK-targeted cancer therapies Nat. Genet. 47(3):250-6. PMID: 25665005
- Weige CC, Birtwistle MR, Mallick H, Yi N, Berrong Z, Cloessner E, Duff K, Tidwell J, Clendenning M, Wilkerson B, Farrell C, Bunz F, Ji H, Shtutman M, Creek KE, Banister CE, Buckhaults PJ. Transcriptomes and shRNA suppressors in a TP53 allele-specific model of early-onset colon cancer in African Americans. Mol Cancer Res. 2014 Jul;12(7):1029-41. doi: 10.1158/1541-7786.MCR-13-0286-T. Epub 2014 Apr 17. PubMed PMID: 24743655; PubMed Central PMCID: PMC4101030.
- Turner-Ivey B, Guest ST, Irish JC, Kappler CS, Garrett-Mayer E, Wilson RC, Ethier SP. (2014) KAT6A, a Chromatin Modifier from the 8p11-p12 Amplicon is a Candidate Oncogene in Luminal Breast Cancer. Neoplasia 16(8):644-55. PMID: 25220592
- Sainski AM, Dai H, Natesampillai S, Pang YP, Bren GD, Cummins NW, Correia C, Meng XW, Tarara JE, Ramirez-Alvarado M, Katzmann DJ, Ochsenbauer C, Kappes JC, Kaufmann SH, Badley AD. (2014)Casp8p41 generated by HIV protease kills CD4 T cells through direct Bak activation. J. Cell Biol. PMID: 25246614
- Kappler CS, Guest ST, Irish JC, Garrett-Mayer E. (2014) Oncogenic signaling in Amphiregulin and EGFR-expressing PTEN-null human breast cancer. Molecular Oncology. DOI: 10.1016/j.molonc.2014.10.006
- Khandelwal N, Breinig M, Speck T, Michels T, Kreutzer C, Sorrentino A, Sharma AK, Umansky L, Conrad H, Poschke I, Offringa R, König, R, Bernhard H, Machlenkin A, Boutros M, Beckhove P. (2015) A high-throughput RNAi screen for detection of immune-checkpoint molecules that mediate tumor resistance to cytotoxic T lymphocytes EMBO Mol Med 7(4):450-63. PMID: 25691366
- Kitambi SS, Toledo EM, Usoskin D, Wee S. (2014) Vulnerability of Glioblastoma Cells to Catastrophic Vacuolization and Death Induced by a Small Molecule. Cell 157:1-16.
- Boettcher M, Lawson A, Ladenburger V, Fredebohm J, Wolf J, Hoheisel JD, Frezza C, Shlomi T. (2014) High throughput synthetic lethality screen reveals a tumorigenic role of adenylate cyclase in fumarate hydratase-deficient cancer cells.BMC Genomics. 15(1):158. PMID: 24568598
- Wolf J, Muller-Decker K, Flechtenmacher C, Zhang F, Shahmoradgoli M, Mills GB, Hoheisel JD, Boettcher M. (2013) “An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation.Oncogene. Advance online publication 2 December 2013; doi: 10.1038/onc.2013.515.
- Wolf J, Dewi D, Fredebohm JA, Muller-Decker K, Flechtenmacher CA, Hoheisel J, Boettcher, M. (2013) “A mammosphere formation RNAi screen reveals that ATG4A promotes a breast cancer stem-like phenotype. Breast Cancer Research. 15:R109 doi:10.1186/bcr3576.
- Fredebohm J, Wolf J, Hoheisel JD, Boettcher M. (2013) Depletion of RAD17 sensitizes pancreatic cancer cells to gemcitabine. J Cell Sci. Aug 1;126(Pt 15):3380-9. doi: 10.1242/jcs.124768. Epub 2013 May 17. PubMed PMID: 23687379.
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.
Plasmid DNA Library:
|Catalog #||Item Description||Amount|
|DHPAC-M1-P||DECIPHER Human Module 1, Pathway Targets||200 μg|
|DHDAC-M2-P||DECIPHER Human Module 2, Disease Targets||200 μg|
|DHCSC-M3-P||DECIPHER Human Module 3, Cell Surface, Extracellular, DNA Binding Targets||200 μg|
|DMPAC-M1V2-P||DECIPHER Mouse Module 1, Pathway Targets||200 μg|
|DMDAC-M2V2-P||DECIPHER Mouse Module 2, Disease Targets (plasmid)||200 μg|
Packaged Viral Library:
|Catalog #||Item Description||Amount Provided|
|DHPAC-M1-V8||DECIPHER Human Module 1, Pathway Targets||2 x 108 TU|
|DHDAC-M2-V8||DECIPHER Human Module 2, Disease Targets||2 x 108 TU|
|DHCSC-M3-V8||DECIPHER Human Module 3, Cell Surface, Extracellular, DNA Binding Targets||2 x 108 TU|
|DMPAC-M1V2-V8||DECIPHER Mouse Module 1, Pathway Targets||2 x 108 TU|
|DMDAC-M2V2-V8||DECIPHER Mouse Module 2, Disease Targets||2 x 108 TU|
|DHPAC-M1-V9||DECIPHER Human Module 1, Pathway Targets||1 x 109 TU|
|DHDAC-M2-V9||DECIPHER Human Module 2, Disease Targets||1 x 109 TU|
|DHCSC-M3-V9||DECIPHER Human Module 3, Cell Surface, Extracellular, DNA Binding Targets||1 x 109 TU|
|DMPAC-M1V2-V9||DECIPHER Mouse Module 1, Pathway Targets||1 x 109 TU|
|DMDAC-M2V2-V9||DECIPHER Mouse Module 2, Disease Targets||1 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
|Catalog #||Item Description||Price|
|CPCP-K2A||Ready-to-Use Lentiviral Packaging Plasmid Mix, 250 μg|
(for 25 10-cm plates)
|LFVC1||LentiFuge™ Viral Concentration Reagent, 1 ml|
(for a total of 1 liter supernatant)
Please email firstname.lastname@example.org for questions or to obtain a quote.