Navigation Links
Setting up Successful siRNA Library Screens


siRNA Libraries Tie Genes to Cell Functions

Ambion has developed human siRNA libraries that target important gene classes including kinases, ion channels, receptor classes, molecular motors, and many others (Figure 1). Applying these siRNA libraries to cell culture screens reveals human genes that are critical for cellular functions. The diversity of cell functions that can be characterized using siRNA libraries is limited only by the range of phenotypic assays that can be developed. With siRNA libraries, you will be able to identify critical human genes faster and easier than ever before.

Figure 1. Ambion siRNA Libraries. [Additional Libraries and Ordering Information]


Scientists at Ambion have already used several Silencer siRNA libraries in quantitative assays to identify genes involved in apoptosis, cell proliferation, TRAIL induction, and p53 activation. Below we provide a general overview of an effective screening process. See Recommendations for Successful siRNA Library Screens, for tips for successful screening experiments.


Overview of the Screening Process

(1) Develop a quantitative assay to monitor cellular process being studied.

Assays that measure the intensity of a cellular phenotype range from microscopic assays that monitor cell size, cell cycle status, or antibody staining; to enzymatic assays that assess the turnover of a specific substrate in a cell lysate; to direct measurements of biomolecules or small molecules in lysates, on cells, or in medium.

A successful screen must use an assay that quantitates a cellular phenotype and maximizes the signal-to-noise ratio. An effective assay must include quality positive and negative control siRNAs. The positive control siRNA should produce the desired phenotype when transfected into cells, and the target of the positive control siRNA should ideally be a gene that is known to act in the process being studied. For instance, if the goal is to identify genes that are involved in a signaling pathway after stimulation by a specific molecule then transfecting an siRNA targeting the receptor for the moleule should disrupt the cell signaling and result in the desired phenotype. Likewise, a negative control siRNA should have essentially no effect on the assay results, which should be comparable to untransfected or mock-transfected cells.

Maximizing signal-to-noise involves testing variables like assay time, assay components (i.e. the reporter), cell type, and length of time between transfection and assay. The greater the difference in assay results between the positive and negative controls, the greater the spread will be in the screening results, and thus, the better the opportunity to i dentify interesting genes.

(2) Optimize transfection conditions for the desired cells.

The first step is to identify a transfection reagent and plating conditions that maximize uptake of active siRNA while maintaining high cell viability. We find it useful to measure both knockdown and cell viability in cells transfected with 2-5 different transfection reagents when using cell lines, or 5-10 electroporation conditions (e.g. varying cell concentration, voltage, pulse length, pulse number, siRNA concentration etc.) when using primary or suspension cells. Transfection can then be optimized for the reagent or electroporation condition that worked best among the conditions tested.

Ambion has several transfection agents developed for effective siRNA transfer to specific cell types; see Enchance Success of siRNA Delivery Into Your Cells and siPORT siRNA Electroporation Buffer for more information. For detailed protocols for chemical transfection and electroporation optimization, see our siRNA Delivery Resource .

Screening siRNAs targeting hundreds of genes requires conditions for high-throughput transfection. siPORT NeoFX facilitates the transfection of up to 1,0 00 wells in less than an hour without the need for robotics (see Streamline Your siRNA Transfections).

(3) Screen

Once the assay and transfection processes have been optimized, a library of siRNAs can be introduced sequentially into cells in a 24 or 96 well plate. Triplicate transfections for each siRNA provide enough data for reasonable statistical analysis. Positive and negative control siRNAs transfected on each plate provide quantitative numbers that will allow data from different plates to be normalized and will provide the range of phenotypes that can be used to identify genes that rate as "hits".

Both positive and negative control siRNAs are available from Ambion. See, RNAi: The Controls You Need for more information.

(4) Validate hits

"Hits" are genes for which an siRNA produces a phenotype that is similar to the positive control. Validating a hit involves showing that the observed phenotype is due to reducing the expression of the target gene. We confirm a hit by individually transfecting three distinct siRNAs targeting the same gene, monitoring reduction in the target mRNA or protein, and then measuring the phenotype. In theory, all siRNAs that similarly reduce the expression of a target gene should yield the same phenotype. In practice, we find occasional off-target sequence effects of siRNAs that lead to false positive or false negative phenotypes for a given siRNA. The use of three individual siRNAs essentially eliminates false positives and false negatives.


back to top


'"/>

Source:


Page: All 1 2 3 4 5

Related biology technology :

1. Setting up the laboratory to avoid contamination
2. Reduce Errors and Save Time When Setting Up PCRs
3. Setting up a kinase profiler with IMAP
4. Keys to Successful Densitometry
5. Successful PCR amplification and subcloning of a GC-rich DNA fragment
6. General Considerations for Successful Transfection Experiments
7. Designing a Successful qRT-PCR Experiment
8. Precursor miRNAs for Successful miRNA Functional Studies
9. Recommendations for Successful siRNA Library Screens
10. Successful stabilization of gene expression profiles
11. Custom and library siRNA for efficient gene silencing
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:2/10/2016)...  The Maryland House of Delegates and House Speaker ... of Maryland School of Medicine Dean E. Albert ... Medical System President and CEO Robert Chrencik , ... honor given to the public by the leader of ... and Mr. Chrencik for their contributions to our ...
(Date:2/10/2016)... (PRWEB) , ... February 10, ... ... REGN) today announced that it has joined the Human Vaccines Project, a ... infectious diseases and cancer. , The Human Vaccines Project brings together ...
(Date:2/10/2016)... 2016  Matchbook, Inc., a company specializing in ... companies, announced today the appointment of Jim ... brings nearly 25 years of experience in supply ... nearly two decades in executive level roles as ... Genzyme and, most recently headed global logistics and ...
(Date:2/10/2016)... ... February 10, 2016 , ... LATHAM, NEW YORK... Marktech Optoelectronics ... Photonics West conference in San Francisco’s Moscone Center from February 16-18, 2016, and ... , These latest InGaAs PIN diode standard packages feature a TO-46 metal can ...
Breaking Biology Technology:
(Date:2/10/2016)... PUNE, India , February 10, 2016 ... --> According to 2016 iris ... fingerprint identification iris recognition is more widely ... are available with both fingerprint and iris ... allows the user to avoid purchasing two ...
(Date:2/5/2016)... DUBLIN , Feb. 5, 2016 /PRNewswire/ ... the addition of the "Global Facial ... offering. --> http://www.researchandmarkets.com/research/5kvw8m/global_facial ) has ... Facial Recognition Market 2016-2020" report to ... Markets ( http://www.researchandmarkets.com/research/5kvw8m/global_facial ) has announced the ...
(Date:2/3/2016)... LIVERMORE, Calif. , Feb. 3, 2016 ... Police Department in Missouri ... of license plate reader (LPR) data from Vigilant Solutions. ... a hit-and-run case in which the victim was walking out ... a parking space next to his vehicle, striking his ...
Breaking Biology News(10 mins):