FlexiTube siRNA

For efficient RNAi analysis one gene at a time


The FlexiTube siRNA is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.
FlexiTube GeneSolution

Cat. No. / ID: 1027416

siRNA GeneSolution details
FlexiTube siRNA (20 nmol)

Cat. No. / ID: 1027419

20 nmol siRNA with modification options delivered in tubes
FlexiTube siRNA (20 nmol)

Cat. No. / ID: 1027418

20 nmol siRNA delivered in tubes
FlexiTube siRNA (5 nmol)

Cat. No. / ID: 1027417

5 nmol siRNA delivered in tubes
FlexiTube siRNA (1 nmol)

Cat. No. / ID: 1027415

1 nmol siRNA delivered in tubes


  • Cost-effective siRNA enables analysis of more genes
  • Optimal solutions for every gene
  • Innovative design minimizes the risk of off-target effects
  • Easy to search for and order siRNA at GeneGlobe

Product Details

Two different FlexiTube products are available: FlexiTube siRNA and FlexiTube GeneSolution.
FlexiTube siRNA is a cost-effective solution for RNAi analysis of small numbers of genes. siRNAs are provided in 5 nmol or 20 nmol amounts for human, mouse, or rat genes, or in economical 1 nmol amounts for human and mouse genes.

FlexiTube GeneSolution is a gene-specific package of 4 preselected siRNAs (1 nmol) for a target gene. FlexiTube GeneSolutions enable researchers to use multiple siRNAs for each target ensuring reliable results. FlexiTube siRNA and FlexiTube GeneSolutions are designed using innovative HP OnGuard siRNA Design and are available at QIAGEN's GeneGlobe Web portal.


Performance guarantee

FlexiTube siRNA comes with a one-time-only replacement offer. If several FlexiTube siRNAs for the same target gene are ordered and at least 2 of them do not provide ≥70% target gene knockdown, QIAGEN will provide 2 additional siRNAs free of charge, once only. You will be asked to provide supporting data, demonstrating that the siRNA failed to knock down the target gene by at least 70% at the mRNA level under appropriate transfection conditions. Supporting data should include transfection efficiency data, quantitative silencing data, and data showing ≥70% knockdown of a positive control. This offer is valid for up to 6 months after the date of delivery.

Thousands of experimentally verified siRNAs

Thousands of our human siRNAs have been experimentally verified by real-time RT-PCR analysis and shown to provide at least 70% knockdown. For these verified siRNAs, experimental details and information about the level of knockdown achieved are provided in GeneGlobe. These experimentally verified siRNAs are the result of the world's largest siRNA validation project, which was carried out by QIAGEN scientists. To find out more about this project, consult the publication Krueger, U. et al. (2007) Insights into Effective RNAi Gained from Large-Scale siRNA Validation Screening. Oligonucleotides 17, 237.

Cutting-edge siRNA design

Advances in the siRNA design process ensure that QIAGEN's highly innovative and sophisticated HP OnGuard siRNA Design delivers potent and specific siRNA. siRNAs are designed using neural-network technology based on an extremely large set of data from RNAi experiments. siRNA design is then checked for homology to all other sequences of the genome using an up-to-date, nonredundant sequence database and a proprietary homology analysis tool. HP OnGuard siRNA Design incorporates many unique and advanced features (see table).

HP OnGuard siRNA Design features
Feature Description References
Neural-network technology siRNA design uses the BioPredsi neural-network, which is based on an extremely large RNAi data set. 1-3
The world's largest siRNA validation project The design process was reinforced and improved by data from this project, in which QIAGEN scientists proved the effectiveness of thousands of siRNAs, were used to . A large number of druggable genome siRNAs have been proven to provide at least 70% knockdown during this project. 4
Homology analysis Analysis uses a proprietary tool and an up-to-date, nonredundant sequence database.  
Affymetrix GeneChip analysis Genomewide analysis enabled development of siRNA design improvements that minimize off-target effects.  
Up-to-date siRNA target sequences Current data from NCBI databases ensure accurate design.  
Asymmetry siRNAs are designed with unequal stabilities of the base pairs at the 5' ends. This enables the antisense strand, which is less tightly bound at its 5' end, to enter RISC, while the sense strand is degraded. Asymmetry produces highly functional siRNAs and reduces the risk of off-target effects caused by the incorrect strand entering RISC. 5, 6
3' UTR/seed region analysis Analysis uses intelligently weighted, multi-parameter searches for matches of the seed region of the siRNA antisense strand with the 3' untranslated region of unintended mRNA targets (see text for further explanation). 7-12
SNP avoidance The RefSNP database is used to exclude siRNAs that span single nucleotide polymorphisms (SNPs). This increases siRNA potency, as an siRNA spanning a SNP will vary in its effectiveness.  
Interferon motif avoidance siRNAs are screened for multiple sequence motifs known to result in an interferon response. siRNAs with such motifs are rejected. 13, 14
3' UTR/seed region analysis

Several studies have shown that off-target effects may be caused by matches of the seed region of the siRNA antisense strand with the 3' untranslated region of unintended mRNA targets (see table). The seed region comprises 6 nucleotides in positions 2–7 of the antisense siRNA strand of the siRNA duplex. Matches such as these can contribute to downregulation of unintended targets due to the siRNA mimicking the action of an miRNA. siRNA designed at QIAGEN is analyzed for 3' UTR/seed region complementarity using a proprietary set of 3' UTR sequences derived from the human, rat, and mouse RefSeq databases. Each siRNA is aligned against these sequences to check for any homology that could contribute to miRNA-like, off-target effects.

Matches of 6 out of 6 nucleotides of the siRNA seed region with an unrelated target 3' UTR sequence are common and it is not necessary or practical to eliminate siRNAs showing such matches. More rarely, seed region matches in combination with 10 or more bases of additional homology are observed in an siRNA sequence. Such homologies have greater potential to result in off-target effects, and where possible these siRNAs are rejected in favor of others with less significant homology to unintended target genes.

For some targets, it is not possible to select siRNAs that do not show any such homologies. In these cases, EntrezGene IDs of the unrelated genes that could be unintended targets of the siRNA are provided at GeneGlobe. Observation of this type of homology does not necessarily mean that these genes will be affected by the siRNA. However, they can be considered potential unintended targets for follow up analysis, if warranted. 


FlexiTube siRNA enables ordering of small numbers of siRNAs at cost-effective 1 nmol amounts (the minimum order is 4 siRNAs), or in 5 nmol and 20 nmol amounts. siRNAs are provided lyophilized in tubes.

FlexiTube GeneSolution for optimal gene-specific solutions

For a streamlined RNAi solution for your target gene, simply enter details of the human or mouse genes of interest at the GeneGlobe Web portal. The search results will display the FlexiTube GeneSolution, which is the 4 recommended siRNAs for each gene provided in 1 nmol amounts. Published guidelines recommend redundancy experiments to ensure accurate reporting of results from RNAi experiments (Echeverri, C.J. et al. (2006) Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat. Methods. 3, 777; Echeverri, C.J. and Perrimon, N. (2006) High-throughput RNAi screening in cultured cells: a user’s guide. Nature Reviews Genetics 7, 373.). Redundancy experiments use several distinct siRNAs targeting different areas of the same mRNA to rule out off-target effects. An off-target phenotype is induced by the specific pattern of cross-silenced transcripts of an siRNA. Since this directly derives from the siRNA sequence, it is highly unlikely that several siRNAs with different sequences will share the same sequence-derived off-target effects. Confirming a phenotype with several distinct siRNAs is an easily applied and convincing way to show siRNA specificity. FlexiPlate GeneSolutions enable redundancy experiments for human and mouse genes. siRNAs are recommended by QIAGEN for each gene so that the optimal solution for your experiments is at your fingertips!

Full siRNA sequence information provided

All siRNAs are provided with siRNA sequence information at no extra charge. Full sequence disclosure provides information for analysis of experimental results and verification of knockdown. siRNA sequences can be included in research publications, if required.

Modification options

FlexiTube siRNAs in 20 nmol amounts are available with labels, including Alexa Fluor, fluorescein, rhodamine, Cy3, and Cy5 dyes, or modification options such as amino linkers, thio linkers, and phosphate modifications.


We recommend HiPerFect Transfection Reagent for low-throughput siRNA transfection and HiPerFect HTS Reagent for high-throughput siRNA transfection.


FlexiTube siRNA and FlexiTube GeneSolution are ideal for functional genomics or pathway analysis with small numbers of gene targets.


How do I calculate the percentage of silencing with real-time RT-PCR for siRNA?

Please find a detailed description for the calculation of the silencing effect in QIAGEN News article 2006 e14 'Real-time RT-PCR for analysis of gene knockdown by RNAi - controls and calculations'.


FAQ ID -498
What is the difference between the 1 nmol FlexiTube and FlexiTube Gene Solution siRNAs?

The siRNA sequences are the same.  With FlexiTube siRNA 1 nmol scale, minimum 4 siRNAs required. It can be any human or mouse, any target, 4  different siRNAs, or the same siRNA.   Whereas 1 nmol FlexiTube GeneSolution is a gene-specific package of 4 pre-selected siRNAs for the same target. 

FAQ ID -3174
How long is fluorescence detectable in cells after transfection with fluorescently labeled siRNAs?

Cells transfected with Alexa-Fluor labeled siRNA still show detectable fluorescence 72 hours after transfection. Certain Alexa dyes, e.g. Alexa Fluor 546, are detectable up to one week after transfection. By comparison, when labeling siRNA with Rhodamine or Fluorescein, transfected cells should be monitored for transfection efficiency after 3-4 hours.

Since Alexa Fluor dyes are more photostable, more resistant to variable pH conditions while in transit through the cell, and much brighter than traditionally used fluorescent dyes, Alexa Fluor labeled HPP Grade siRNA is the ideal choice for monitoring transfection efficiency.

For data and additional details on using fluorescently labeled siRNA, refer to QIAGEN News article e20, 2004: 'Alexa Fluor labeled siRNA is highly effective for monitoring transfection efficiency'.

FAQ ID -392
What are the critical factors in designing the siRNA molecules to be used for RNAi studies?
The algorithm utilized to design the siRNA of interest must assure both exquisite gene-specificity (to minimize off-target effects) and potent efficacy (expression knock down). A minimum of two siRNA molecules must be used for each gene of interest, in order to confirm the gene specificity of any observed changes.
FAQ ID -2759
What is the difference between various FlexiTube siRNAs listed for the same target gene, and which one should I choose?

Different Flexitube siRNAs for the same target gene vary slightly in their nucleotide sequence and exact position along the target. All of them were selected by the unique HiPerformance siRNA Design Algorithm and thus have a very high likelihood for knocking down the target gene efficiently. Knockdown achieved with siRNA designed by the HiPerformance algorithm is usually greater than 70%.

Consequently, any of the FlexiTube siRNAs listed in GeneGlobe for a given gene can be chosen for knockdown experiments. We strongly recommend to try at least two siRNAs for independent confirmation that the observed effects are due to specific knockdown of the targeted gene.

Flexitube siRNA comes with a one-time–only replacement offer. If 2 or more HP GenomeWide siRNAs for the same target gene are ordered and none of the siRNAs result in gene silencing, QIAGEN will provide 2 additional siRNAs free of charge, once only. Please visit our website, or contact QIAGEN Technical Services for details and required proof data.

FAQ ID -1206
Do I need to resuspend FlexiTube siRNAs in siRNA Resuspension buffer?

You just need to add sterile RNase-free water (which is supplied with your siRNAs) to resuspend your FlexiTube siRNA. You do not need to perform incubation steps at 96°C or at 37°C. Your siRNA comes preannealed and does not need any further preparation prior to use.


FAQ ID -1659
Can I still reorder siRNA that has been removed from the GeneGlobe data base?

Some siRNAs have been deleted from our standard GeneGlobe offering. For those siRNAs, the entries in public databases may have changed and the transcript is no longer listed in those databases. In other cases, we have added siRNAs with a new design.

You can still find previously listed siRNAs in GeneGlobe by searching for the specific SI number (ordering number). See also FAQ 1366 on this topic.


FAQ ID -1668
Do I need to anneal, deprotect or desalt my QIAGEN siRNA?

QIAGEN siRNA is delivered as a stable, ready-to-use duplex and does not need to be deprotected, desalted, quantified, or annealed before use. Simply resuspend the lyophilized RNA in the sterile RNAse-free water provided and transfect. Instructions for preparing your siRNA are provided on the data sheet supplied with each siRNA shipment.

FAQ ID -398
What criteria should one use in choosing between siRNA versus shRNA for their studies?

This decision is based on two key factors – the “transfectability” of the target cells, and the desired duration of the experiment.

siRNA molecules work well for high throughput, transient studies, with cells that are easily transfected. The limitations of using siRNA are two-fold. First of all, they do not work well with a few cell types that are extremely difficult to transfect. In addition, their use is restricted to experiments studying the impact of transient suppression of gene expression.

shRNA are carried within the context of a plasmid or viral-based vector, they can be engineered to carry a reporter gene. A reporter gene provides a straightforward readout, for carrying out transfection optimization studies. In addition, a fluorescent reporter gene (such as GFP) allows the use of fluorescence-activated cell sorting (FACS) to enrich for transfected cells. Alternatively, the vector may carry an antibiotic-resistance gene, which permits the selection of a stably transfected cell population. Another obvious advantage to using a vector-based shRNA construct is that it provides a renewable source of reagent for subsequent RNAi studies.

The key benefit of using viral-based shRNA delivery vectors is that they can efficiently deliver the shRNA into cells that are difficult (or impossible) to transfect. Additionally, viral transduction is a much more efficient process than transfection.

FAQ ID -2771
Are Northern Blots sensitive enough to detect siRNA-induced gene silencing?

Yes, Northern Blot Analysis has been shown in the literature to detect siRNA-induced reduction of specific mRNA. Whether a Northern Blot will be sensitive enough to detect a mRNA under investigation mainly depends on the expression level of the respective gene in the untreated control.

You can find an example for this application in the reference "Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems". Caplen et al., PNAS 2001, vol. 98, no. 17, pages 9742-9747.

We recommend to perform real-time RT-PCR for exact quantification of mRNA expression levels.

FAQ ID -403
Can HP Validated siRNAs be ordered on the FlexiPlate?

Yes, you can order HP GenomeWide siRNAs and HP Validated siRNAs with the Flexiplate siRNA format. There is no price difference between HP GenomeWide siRNAs and HP Validated siRNAs ordered as FlexiPlate siRNA. For HP Validated siRNAs, no sequence information is provided.


FAQ ID -1367
Do you have a protocol for the fixation of cells transfected with fluorescently labeled siRNA?

For the fixation of cells transfected with fluorescently labeled siRNA, we would suggest to perform the following protocol:

  1. After transfection, remove the medium from the cells and wash the cells once with PBS.
  2. Incubate the cells for 15 minutes at room temperature with 4% Paraformaldehyde (in PBS, pH 7.0). The cells should be completely covered by this solution (e.g., for a 96-well plate use 50 µl solution/well)
  3. Wash the cells with PBS.

Fixed cells can be stored at 4°C for a few days.

(Note: It is also possible to use chamber slides or object slides for this procedure. Object slides should be coated to provide better growing conditions for cells. Cells can be fixed as described above and then overlayed with embedding medium to allow investigation using a fluorescence microscope. Optimal conditions for this method need to be determined by the user)


FAQ ID -793
Which siRNA controls are available in FlexiTube format?
siRNA Controls available in FlexiTube format are:

Mm/Hs_MAPK1 control siRNA (5 nmol)    cat. no. 1022564

GFP-22 siRNA (5 nmol)    1022064

Luciferase GL2 siRNA (5 nmol)     1022070

Luciferase GL3 siRNA (5 nmol)     1022073

Negative Control siRNA (5 nmol)      1022076

AllStars Negative Control siRNA (5 nmol)     1027280

AllStars Neg. Control siRNA (20 nmol)        1027281

AllStars Neg. siRNA AF 488 (5 nmol)         1027284

AllStars Neg. siRNA AF 546 (5 nmol)         1027285

AllStars Neg. siRNA AF 555 (5 nmol)         1027286

AllStars Neg. siRNA AF 647 (5 nmol)          1027287

AllStars Neg. siRNA AF 488 (20 nmol)         1027292

AllStars Neg. siRNA AF 546 (20 nmol)          1027293

AllStars Neg. siRNA AF 555 (20 nmol)          1027294
AllStars Neg. siRNA AF 647 (20 nmol)          1027295

AllStars Hs Cell Death Control siRNA (5 nmol)     1027298

AllStars Hs Cell Death Control siRNA  (20 nmol)    1027299

Negative Control siRNA (20 nmol)                 1027310

Mm/Hs_MAPK1 control siRNA (20 nmol)          1027321

FAQ ID -1661
Are FlexiTube siRNA and FlexiTube GeneSolution also available for rat siRNAs?

 FlexiTube siRNA is available for human, mouse and rat genes at 5 nmol and 20 nmol scale. FlexiTube GeneSolution and FlexiTube siRNA at 1 nmol scale are available for human and mouse genes only

FAQ ID -1664
Can FlexiTube siRNA or FlexiTube GeneSolution products be ordered in solution?

No, FlexiTube siRNA and FlexiTube GeneSolution products are only shipped lyophilized at room temperature. We do not offer these products in a different format.



FAQ ID -1667
What are the structures of the siRNA molecules used in RNAi studies?
The nature of the molecules used in RNAi studies fall into two classes. The first is chemically synthesized siRNA. Typically, these are 21 nt dsRNA molecules with phosphorylated 5’ ends and 3’ dinucleotide overhangs, which directly function as templates for RISC formation. These molecules are introduced via chemical or electroporation-based transfection, and mediate a transient suppression of gene expression. The second class of molecules are shRNA (short hairpin RNA). These are typically delivered to the cell as part of a plasmid or viral vector. The shRNA molecules induce an RNAi effect by serving as substrates for the cytoplasmic RNase, Dicer.
FAQ ID -2760
Can I select HP Validated and HP GenomeWide siRNAs for FlexiTube?

Yes, you can select from HP Validated and HP GenomeWide siRNAs for the FlexiTube format. There is no price difference.


FAQ ID -1658
Where can I find QIAGEN products for a specific gene or gene product?
You can search for specific gene products in the QIAGEN GeneGlobe Database. This easy-to-use, comprehensive Web portal allows you to find information about, search for, and order high-quality products for human, mouse, and rat genes. QIAGEN provides a vast range of gene-specific products covering every aspect of an experiment, from gene silencing to expression analysis at the mRNA or protein level.
FAQ ID -803
How do I submit a siRNA order by telephone or online?

FlexiTube siRNA, FlexiTube GeneSolution, FlexiTube siRNA Premix, FlexiPlate siRNA, and GeneFamily Lists siRNAs can be ordered by catalog number over the telephone.

However, to ensure accuracy, Custom siRNA Synthesis orders should be submitted in writing. Therefore you can use the HP Custom siRNA Order Form https://www.qiagen.com/products/genesilencing/customsirna/customsirnaorder.aspx?EmailOrdering=1.

Visit the RNAi Solutions page http://www.qiagen.com/products/rnai/default.aspx?r=2714 on our homepage for access to the Online Ordering Tool, and choose the order link for your product of interest.

FAQ ID -399
If I am working with a difficult-to-transfect cell type or if I obtain only weak silencing effects what can I do?
In the case of difficult cell types or weak silencing effects, it may be helpful to increase the final siRNA concentration during transfection. This can be achieved simply by using larger amounts of FlexiTube siRNA Premix for transfection.
FAQ ID -2265
Do you have information on in vivo RNA interference experiments?

Yes. Please see the QIAGEN News Article (2005 e3) "RNAi - a promising tool for target validation studies and therapeutics" to learn about the most recent advances in this field. It provides numerous references for the aspects of in vivo siRNA delivery and siRNA stability as well as in vivo RNAi in general. QIAGEN offers economical, high-purity siRNA compatible with in vivo animal delivery systems for reliable World-class RNAi solutions.



FAQ ID -817
Can the MAPK1 control siRNA be used for rat cells?
No. The Mm/Hs_MAPK1 control siRNA is specific for mouse and human MAPK1 only. Please visit GeneGlobe to search for all currently available gene-specific products for RNAi.
FAQ ID -547
Is sequence information for HP Validated siRNAs provided in the FlexiTube format?

Yes, sequence information for FlexiTube is provided both for HP GenomeWide siRNAs and HP Validated siRNAs, in the enclosed paper documentation upon delivery.




FAQ ID -1665
Are your FlexiTube siRNAs preferentially designed to any particular region of the target gene?

No, the design of Flexitube siRNAs in GeneGlobe is not biased towards either the 3' or the 5' end of the target gene.

A number of siRNAs are located in the 3' untranslated region for optimized specificity of the siRNA sequences to their target gene. Since there are homologous sequences in the coding regions of other genes for many targets, it is usually easier to find highly unique siRNA sequences in the untranslated regions. Such design ensures highly specific silencing effects for the gene of interest. 

FAQ ID -1091
What is the most reliable transfection reagent for delivering shRNA plasmids and siRNA to cells in culture?

HiPerFect Transfection Reagent is optimized for siRNA transfections and enables effective siRNA uptake and efficient release of siRNA inside cells, resulting in high gene knockdown even when using low siRNA concentrations. For high-throughput siRNA screenings HiPerFect HTS Reagent is a fast and effective newcomer specifically designed to focus on robustness and cost efficiency. For the transfection of shRNA.

Attractene Transfection Reagent should be used for the transfection of shRNA (short-hairpin RNA) vectors for gene silencing experiments to achieve high efficiency. Ease and flexibility of handling enables preparation and storage of transfection complexes making Attractene Reagent suitable for use with automated systems.


FAQ ID -2777
Is FlexiTube GeneSolution available for other scales than the 1 nmol scale?
FlexiTube GeneSolution is only available at the 1 nmol scale in tubes.
FAQ ID -1666
Has RNAi been successful using siRNA in Zebrafish and Xenopus?

Here are examples of references that describe the inhibition of gene expression by siRNA in Xenopus and Zebrafish:

FAQ ID -400
What are the sequences of the FlexiTube siRNAs?

You will receive the sequences of the FlexiTube siRNAs on the data sheet along with your order.

A graphic representation of the position of HP GenomeWide siRNAs along the target sequence is available for numerous genes on our website. It can be accessed via GeneGlobe after pulling up the target gene of interest, clicking on the 'Gene Symbol' link for the species of interest, and then clicking the link under 'Product name' for details on the gene product of interest.

FAQ ID -851