General Articles

Protocols

Care and Handling of siRNA Oligonucleotides
Description:
All reagents used in the synthesis and purification of Ambion's siRNA are tested and certified nuclease-free. However, RNA oligonucleotides are susceptible to degradation by exogenous ribonucleases introduced during handling.

Technotes

A New Way to Assess siRNA Delivery Efficiency  -  TechNotes 12(3)
Description: With our new KDalert™ GAPDH Assay Kit and a microplate fluorometer you can obtain a reliable measure of GAPDH enzyme activity in cultured human, mouse, or rat cells in less than 30 minutes.

Are siRNA Pools Smart?   -  TechNotes 12(1)
Description: Two strategies for large-scale screening experiments are compared.

Assessing Gene Function with siRNA Libraries  - TechNotes 11(3)
Description: An experiment is described in which siRNAs from the Silencer™ Kinase siRNA Library were each tested to determine their effects on cellular proliferation and mitotic index.

Cells-to-cDNA™ II Applications | Quantitation of siRNA Target Gene Expression
Description: Quantitate gene expression in siRNA transfected cells without isolating RNA

Controlling Variability in Cell Assays When Designing RNAi Experiments

Control Your siRNA Research | Proven siRNA Controls and Matched Primary Antibodies  - TechNotes 10(1)
Description: Ambion introduces a control siRNA targeting ß-actin, as well as a primary antibody against ß-actin ideal for use in immunofluorescence experiments to detect the reduction in protein levels induced by RNAi.

Delineating the Role of Survivin in Oncogenesis: An siRNA Study   -  TechNotes 13(4)
Description: In this study, targeted siRNAs were used to alter survivin expression, and a series of biochemical and cell-based assays were performed on the transfected cells to assess known indicators of apoptosis to better understand the role of survivin in cancer.

Duration of siRNA Induced Silencing: Your Questions Answered   -  TechNotes 15(3)
Description: In this article we answer questions regarding the persistence of the RNAi effect initiated by transfecting siRNAs into human cells.

Enhanced siRNA Delivery and Long-term Gene Silencing  -  TechNotes 12(1)
Description: Use Ambion's new pSilencer™ 5.1 Retro System to stably express siRNAs from a retroviral vector

Ensure RNAi Success  -  TechNotes 13(4)
Description: Together, Ambion and Applied Biosystems provide a complete and convenient solution for gene silencing experiments.

Experimental Variability and Replicates in siRNA Experiments   -  TechNotes 14(4)
Description: This article describes different sources of variation in RNAi experiments, as well as how to determine the ideal number of replicates.

Fast and Accurate Confirmation of Gene Silencing | Silencer® siRNAs & TaqMan® Gene Expression Assays  -  TechNotes 14(1)
Description: This article illustrates the combined use of Ambion’s Silencer® siRNAs and Applied Biosystems TaqMan® Gene Expression Assays to generate high quality, accurate, and reproducible gene silencing data.

Fast Accurate Assessment of siRNA-induced Gene Silencing   - TechNotes 12(2)
Description: This article illustrates the combined use of Ambion’s Silencer® siRNAs and Applied Biosystems TaqMan® Gene Expression Assays to generate high quality, accurate, and reproducible gene silencing data

Five Ways to Produce siRNAs   -  TechNotes 10(3)
Description: An overview of five methods for generating siRNAs for use in gene silencing studies.

Fluorescently Label Your siRNA to Track it in Live Cells  -  TechNotes 9(4)
Description: Label siRNAs with Cy3 or FAM for analysis of subcellular localization, transfection efficiency and to identify transfected cells for further analysis.

Gene Specific Silencing by RNAi  - TechNotes 10(1)
Description: A brief overview (with figure) of the mechanism of RNAi.

Get Control of Your siRNA Experiments
Description: Applied Biosystems R&D personnel offer advice on the proper use of controls for siRNA experiments.

Getting Started with RNAi  - TechNotes 13(1)
Description: A sampling of the introductory information found in Ambion's newly available RNA Interference Research Guide.

Getting Started with RNAi In Vivo  -  TechNotes 15(2)
Description: This article describes an RNAi experiment in an animal model in which siRNA was administered using hydrodynamic tail vein injection.

High Throughput Delivery of siRNAs: Examples   -  TechNotes 12(3)
Description: View siRNA screening data from a recent Ambion publication which was used to identify kinase genes involved in cell proliferation.

Matched siRNAs and Assays   -  TechNotes 11(4)
Description: Ambion siRNAs eliminate the guesswork associated with siRNA design and testing, while Applied Biosystems' Taqman® Gene Expression Assays provide a fast, simple way to measure mRNA knockdown

Next Generation siRNAs to Make Your Silencing Roar - TechNotes 15(1)
Description: Ambion® Silencer® Select siRNAs incorporate the latest improvements in siRNA design, prediction algorithms for off-target effects, and chemical modifications to yield siRNAs with unrivaled efficacy, potency, and specificity.

Optimizing siRNA Transfection for RNAi   -  TechNotes 12(1)
Description: 
Low transfection efficiency and low cell viability are the most frequent causes of unsuccessful gene silencing experiments.

Performing RNAi Experiments in Animals  -  TechNotes 13(1)
Description: An introduction to RNAi in vivo, including discussion of local administration and systemic delivery of siRNAs.

Quickly Assess siRNA Delivery and Cell Viability in the Same Assay  -  TechNotes 13(1)
Description: Ambion's KDalert™ GAPDH Assay is simple 3-step procedure for the quantitation of siRNA induced GAPDH knockdown in cultured cells, making this kit the ideal tool for transfection optimization experiments.

RNAi Four-Step Workflow  - TechNotes 15(1)
Description: This brief article outlines the workflow for a typical RNAi experiment using siRNAs.

RNAi as a Tool for Mammalian Gene Analysis: Applications of siRNAs   -  TechNotes 10(5)
Description: An Ambion senior scientist discusses some of the more prominent applications for RNAi in mammalian systems and examples of these applications from the literature.

RNAi: Size Does Matter  -  TechNotes 9(5)
Description:  How dsRNA length correlates with gene silencing efficiency

Recommendations for Successful siRNA Library Screens  -  TechNotes 11(6)
Description: Ambion scientists identify five procedures that significantly improve siRNA library screen results.

Reduced siRNA Concentrations Lead to Fewer Off-Target Effects  -  TechNotes 15(2)
Description: Silencer® Select siRNAs are designed for higher potency and specificity and fewer off-target effects, leading to the attainment of maximum knockdown with lower concentrations of siRNA.

Reproducibly Deliver siRNAs into Cultured Cells  -  TechNotes 14(2)
Description: siPORT™ NeoFX™ is a lipid-based transfection agent that can be used to efficiently transfect adherent cells as they are subcultured—without increased cytotoxicity.

RNAi How To for New Users  -  TechNotes 11(5)
Description:
RNA interference, the biological mechanism by which double-stranded RNA (dsRNA) induces gene silencing by targeting complementary mRNA for degradation, is revolutionizing the way researchers study gene function.

Selecting siRNA Sequences to Incorporate into the pSilencer Vectors   -  TechNotes 9(5)
Description: A guide to the identification of target gene sequences that are susceptible to siRNA-induced degradation.

Setting up Successful siRNA Library Screens    -  TechNotes 11(6)
Description: A general overview of an effective screening process.

Silencer® siRNA Libraries | siRNA Libraries Targeting Important Functional Gene Classes
Description: New versions of Ambion's 0.25 nmol size Silencer® siRNA Libraries have been released. Learn the details in this article, including the number and types of genes targeted by each library.

Silencer® siRNA Screening Control Panel | Effective Controls for RNAi Screening Experiments  - TechNotes 13(1)
Description: An overview of Ambion's new Silencer® siRNA Screening Control Panel of positive and negative control siRNAs for determining transfection efficiency and hit thresholds in siRNA screening experiments.

Silencer® siRNA Starter Kit | New User's Kit for Gene Silencing   -  TechNotes 13(1)
Description: Silencer siRNA Libraries are sets of siRNAs targeting groups of genes from functional gene classes to whole genomes, so they are ideal for pathway analysis and target identification and validation.

Silencer® siRNA Libraries | Shine the Light on Gene Function  -  TechNotes 14(2)
Description: Silencer siRNA Libraries are sets of siRNAs targeting groups of genes from functional gene classes to whole genomes, so they are ideal for pathway analysis and target identification and validation.

siRNA Expression Vectors with Selectable Markers  - TechNotes 10(1)
Description:
Six new pSilencer™ siRNA expression vectors are now available, each with an antibiotic resistance gene to facilitate selection in mammalian cultured cells.

siRNA Screening Validate Thousands of Targets in a Single Week   - TechNotes 16(1)
Description: Validation of siRNA knockdown can often take longer than the screen itself. Two Applied Biosystems scientists have streamlined this step more than 10-fold, validating over 1500 siRNAs targeting more than 500 genes within a single week.

siRNA Design It's All in the Algorithm   - TechNotes 11(3)
Description: The effectiveness of the algorithm used to design Ambion's Silencer™ Pre-designed, Validated and Library siRNAs is demonstrated with approximately 1100 different siRNAs and 400 endogenous transcripts.

siRNA-Induced mRNA Knockdown and Phenotype: How to Measure and When to Measure -  TechNotes 15(3)
Description: In this report, Applied Biosystems scientists investigated the duration of an expected phenotype in parallel with the measurement of mRNA knockdown at various time points after siRNA transfection.

Streamline Your siRNA Transfections  - TechNotes 11(6)
Description: Introducing siPORT™ NeoFX™ Transfection Agent for fast, reproducible transfection of siRNA.

Test More siRNAs for Less  -  TechNotes 9(6) 
Description: Ambion's new Silencer™ siRNA Contruction Kit produces transfection-ready siRNA at a fraction of the cost of chemical synthesis.

Tools for Optimizing siRNA Delivery | Define the Best Conditions for siRNA Delivery in Cultured Cells   -  TechNotes 14(2)
Description: Ambion siRNA delivery optimization kits and reagents are easy to use and include detailed instructions to help you streamline the optimization process.

Understanding Calculations for siRNA Data  -  TechNotes 14(3) Description: This article describes how to determine the percent remaining gene expression and percent knockdown of gene expression when assessing the effects of siRNAs with real-time RT-PCR.

Using Validated siRNAs in Functional Genomic Assays  -  TechNotes 10(3)
Description: A Silencer Validated siRNA targeting the TNFalpha receptor is used to identify gene products associated with TNFalpha-induced activation of the NF-kappaB pathway.

Visualizing siRNA in Mammalian Cells  -  TechNotes 9(3)
Description:
Labeling GAPDH and c-myc siRNA with either fluorescein or Cy3 was demonstrated to have no effect on silencing efficiency, but allowed visualization of the distribution patterns of these molecules after transfection.

Which Competent Cells to Use for Cloning siRNAs into pSilencer
Description: Applied Biosystems R&D personnel offer advice on the proper use of controls for siRNA experiments.