Download Genome-scale RNAi screens now at your benchtop Decode RNAi

Decode TM RNAi viral screening libraries
Genome-scale RNAi screens
now at your benchtop
Overview of positive and negative selection
screens using Decode RNAi screening libraries
Decode RNAi viral screening libraries combine the
advantages of shRNAmir design, the power of viral delivery
and the convenience of ready-to-use viral pools. Optimized
for positive or negative selection (dropout) screens, this
format is a cost-effective solution for multiplexed RNAi.
Advantages include:
Efficient single copy knockdown essential for
multiplex screening strategies
Ready-to-use high titer viral pool format
Lentiviral delivery extends RNAi screening
to primary and non-dividing cells
Easily identified hits via barcode microarrays
(negative selection) or shRNA sequencing
(positive selection)
Decode RNAi viral pool specifications
Each screening pool contains -10,000 unique shRNAmir
expressing viral particles. Viral titers of each pool are
greater than 5x10A8TU/ml. Depending on the target cell line
used, one Decode RNAi viral screening kit contains enough
virus to perform at least two screens in triplicate.
Pooled viral screening format is available for the human
G1 P2 lentiviral shRNAmir library.
Whole genome
(7 pools of 10,000 constructs each)
Highly annotated genes
(3 pools of 10,000 constructs each)
Decode RNAi barcode microarray
Decode RNAi barcode microarrays contain the reverse
complement of barcode sequences optimized for minimal
cross hybridization. Two microarrays in 2x105k format are
provided with each negative selection kit. This allows four
dual label hybridizations with 58,498 unique barcodes
represented.
Positive selection screening strategies identify
those shRNAmir whose expression allows a cell to be
isolated from a population of cells. The most common
methodology employs a lethal selective pressure
utilizing survival as a distinguishing phenotype.
However, any distinguishing phenotype (e.g.
expression of a ligand or other indicator) can be used
if it allows a cell to be isolated from a population of
cells. The benefit of this type of screen is its
stringency and ability to be performed without
additional technology.
Negative selection (Dropout) screening strategies
identify those shRNAmir whose expression modulates
the growth of cells. The benefit of this screen is that it
captures both positive and negative effects (missed
by a positive screen) on the growth of cells.
Single Copy Knockdown with Lentiviral
shRNAmir
pGIPZ Vector Details
Decode RNAi screening library kit
Schematic of the pG1P2 vector is shown above. Only elements
between the LTR's are present in the viral particles.
G1P2 lentiviral shRNAmir have been shown to produce effective
knockdown at low copy. The data above shows knockdown
achieved at multiplicity of infection (MO1) of 0.3-2. This study
was done as part of a validation project sponsored by the NC1.
Catalog
Description
RHS4847
Decode RNAi-GIPZ: whole genome screening
library-Positive selection kit
RHS5337
Decode RNAi-GIPZ: whole genome screening
library-Negative selection kit
RHS5338
Decode RNAi-GIPZ: annotated genes
screening library-Positive selection kit
BCA5101
Decode RNAi-GIPZ: annotated genes
screening library-Negative selection
kit
Decode RNAi Barcode microarray - Human
RHS4348
Non-silencing-GIPZ lentiviral shRNAmir
control - Viral particles
RHS5339
contents
Positive selection kits include:
/. Decode RNAi lentiviral pools* each containing
10,000 G1P2 lentiviral shRNAmir
2. Non-silencing control shRNAmir lentiviral
particles
3. PCR primers for shRNAmir amplification
4. Plasmid DNA for PCR positive control
5. Sequencing primers for identification of
positive shRNAmir hits
Negative selection kits include:
/. Decode RNAi lentiviral pools* each containing
10,000 G1P2 lentiviral shRNAmir
2. Non-silencing control shRNAmir lentiviral
particles
3. PCR primers for barcode amplification
4. 2 barcode microarrays for deconvolution of
hits
*Whole genome kit contains 7 pools
*Annotated gene kit contains 3 pools
Published multiplexed RNAi screens using Open Biosystems' shRNAmir pools
Westbrook T et al2005 "A Genetic Screen for Candidate Tumor Suppressors 1dentifies REST" Cell, Vol. 121, 837-848.
Gazin C et al2007 "An elaborate pathway required for Ras-mediated epigenetic silencing" Nature Vol 449: 1073-1077.
Silva JM et al2008 "Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening" Science Vol 319, 617-620.
Schlabach M et al2008 "Cancer Proliferation Gene Discovery through Functional Genomics" Science Vol 319, 620-624.
Gobeil S et al2008 "A genome-wide shRNA screen identifies GAS1 as a novel melanoma metastasis suppressor gene" Genes
Dev., Vol 22:2932-2940.