ExpiFectamine™ 293 Transfection Kit, For 1 L of culture - FAQs

I left my DNA-ExpiFectamine 293 transfection complexes sit longer than 20 minutes. Will they be okay?

The best transfection efficiencies are obtained when transfection complexes are used fresh. However, they should be stable for at least an hour.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

I ran out of OptiPRO SFM. Can I use use Opti-MEM I Reduced Serum Medium to make my DNA-ExpiFectamine 293 transfection complexes?

We do not recommend using OptiPRO SFM to make DNA-ExpiFectamine 293 transfection complexes. If you require an animal origin-free system, you may use FreeStyle 293 Expression Medium to make the complexes, but keep in mind that there will be a 10-20% drop in final protein yields.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Can FreeStyle 293-F cells grown in FreeStyle 293 expression medium be transfected with ExpiFectamine293 Reagent along with enhancers? Is so, will the transfection efficiency be higher than that with FreeStyle Max Reagent?

You should be able to use the ExpiFectamine293 Reagent for transfection of Freestyle 293-F cells grown in FreeStyle 293 Expression Medium; however, the enhancers will provide only a little boost in expression as they are designed to work with higher density cultures that FreeStyle 293 Expression Medium cannot support.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What is the stability of DNA-ExpiFectamine 293 transfection complexes?

The best transfection efficiencies are obtained when transfection complexes are used fresh. However, they should be stable for at least an hour.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

How many days should I wait before harvesting my protein in the Expi293 Expression System?

The optimal expression time will be different for each protein, but most tested proteins fall within a 3-7 day window. As the system scales well, it is recommended you run a small-scale pilot experiment to determine when to harvest your protein of interest prior to scaling up.

Find additional tips, troubleshooting help, and resources within our Protein Expression Support Center.

Can I purchase the ExpiFectamine 293 Transfection Enhancers 1 & 2 separately?

No, you cannot purchase the enhancers separately. They are only sold as part of a kit (with ExpiFectamine 293 Reagent).

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Can I use the ExpiFectamine 293 Transfection Enhancers 1 & 2 with other transfection reagents to boost my transfection efficiency?

The ExpiFectamine 293 Transfection Enhancers 1 & 2 are designed to work with the ExpiFectamine 293 Reagent and do not work well with other transfection reagents.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Can I use OptiPRO SFM instead of Opti-MEM I Reduced Serum Medium to make my DNA-ExpiFectamine 293 transfection complexes?

We do not recommend using OptiPRO SFM to make DNA-ExpiFectamine 293 transfection complexes. If you require an animal origin-free system, you may use FreeStyle 293 Expression Medium to make the complexes, but keep in mind that there will be a 10-20% drop in final protein yields.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What is the role of the Transfection Enhancers supplied in the ExpiFectamine 293 Transfection Kit?

The ExpiFectamine 293 Transfection Enhancers 1 & 2 are optimized cocktails of proprietary reagents designed to work with the ExpiFectamine 293 Reagent to increase protein expression levels and hence transient protein yields. They must be added at the appropriate time (20 hours post-transfection) to obtain maximal protein yield. Addition of enhancers earlier or later will result in lower protein yields. If you forget to add enhancers during the recommended time window, we recommend adding them as soon as possible. Omission of the enhancers from the protocol can cause protein yield to be up to 3-fold lower. The enhancers are designed to work together for maximal expression. Addition of just one enhancer will result in reduced expression and may be anywhere from one-third to two-thirds the level of expression obtained when both enhancers are added.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

I accidentally left my lipid reagent at room temperature. Can I still use it?

Yes, all of our lipid transfection reagents are stable at room temperature for months.

Find additional tips, troubleshooting help, and resources within our Lipid-Based Transfection Support Center.

What is the difference between reverse transfection and forward transfection? What should I use?

In forward transfection, cells are seeded to appropriate confluence or cell density in wells or dishes, and the lipid-DNA complexes are added the next day. In reverse transfection, the transfection complexes are prepared inside the wells, after which cells and medium are added. Reverse transfection is faster to perform than forward transfection, and is the method of choice for high-throughput transfection. For non-high-throughput transfections, generally forward transfections have better efficiency for most cell types.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Is there a place where I can find references from other researchers who have used your transfection reagents?

Visit the product page for each reagent type and you will see a list of references at the bottom of the page. A table that lists specific cell line references is also accessible. We also recommend www.highwire.org as a search engine to find a large selection of up-to-date research articles using our transfection products. Simply include the name of the transfection reagent and your cell line/application of interest in your search criteria.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Can I use antibiotics in the medium during transfection?

Antibiotics can be used in the medium for culturing of cell lines. However, we do not recommend using antibiotics in the transfection medium unless previously tested in the cell type and payload being transfected. This is because presence of antibiotics during transfection may adversely affect transfection efficiency (i.e., positively charged antibiotics binding to the DNA being transfected) and overall health of cells being transfected.

For stable transfection, we recommend waiting wait 24-48 hrs after transfection before adding selected antibiotics.

Find additional tips, troubleshooting help, and resources within ourTransfection Basics Support Center.

Is it necessary to use serum-free medium during lipid transfection?

It is not necessary to use serum-free medium during lipid transfection. However, it is critical to form the lipid:nucleic acid complex in the absence of serum, because proteins can interfere with complex formation. Once the complexes are formed, they can be added to cells in serum-containing medium. For optimal results with Lipofectin Transfection Reagent, we recommend performing transfection in medium without serum.

Find additional tips, troubleshooting help, and resources within our Lipid-Based Transfection Support Center.

What kind of tubes should I use for making lipid:DNA complexes?

Polypropylene, polystyrene, or glass tubes may be used with any of our transfection products without issue.

Find additional tips, troubleshooting help, and resources within our Lipid-Based Transfection Support Center.

Which lipid transfection reagent would you recommend to use for my cell line?

We recommend using Lipofectamine 3000 Reagent (Cat. No. L3000015) for the delivery of plasmid DNA, Lipofectamine MessengerMAX Reagent (Cat. No. LMRNA001) for mRNA or short oligos, and Lipofectamine RNAiMAX Reagent (Cat. No. 13778150) for siRNA or miRNA. Please refer to the Transfection reagent selection guide (http://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-reagent-application-table.html) to choose the best reagent based on cell type and application.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What controls do you recommend that I use when performing a transfection?

To ensure optimal transfection success, we recommend including a positive transfection control and additional controls to confirm cell health and reagent quality.

For DNA transfection, we recommend using the pJTI R4 Exp CMV EmGFP pA Vector (Cat. No. A14146). For siRNA transfection, we recommend using either the BLOCK-iT AlexaFluor Red Fluorescent Control (Cat. No. 14750100) or Silencer Select GAPDH Positive Control siRNA (Cat. No. 4390850). For protein transfection, we recommend co-transfecting with an EmGFP mRNA such as the Tri-Link CleanCap EGFP mRNA (Cat. No. L-7201).

Cell health and reagent quality controls:
- Cells only
- Cells + DNA or RNA or protein only
- Cells + lipid reagent only
- Cells + Opti-MEM only
- Cells + positive control

Find additional tips, troubleshooting help, and resources within ourTransfection Support Center.

What points should I consider to achieve optimal transfection with a lipid-based transfection reagent?

Here are some points to consider:

1. Select the lipid reagent that is likely to result in highest transfection efficiency for your cell type, payload, and application. Please refer to the Transfection Reagent Selection Guide (https://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-reagent-application-table.html) to choose the best reagent.
2. Optimize both lipid reagent and DNA quantities. The most important parameter after the condition of the cells is the ratio of lipid to DNA.
3. Do not use serum during complex formation. Serum may contain components that could interfere with complex formation. We recommend using Opti-MEM I Reduced-Serum Medium for optimal complex formation. However, serum-free DMEM or serum-free RPMI 1640 Medium can be used, but the efficiency of complex formation may not be as high as with Opti-MEM I Reduced-Serum Medium.
4. Do not use antibiotics, EDTA, citrate, phosphate, chondroitin sulfate, hyaluronic acid, dextran sulfate, or other sulfated proteoglycans in the medium used to prepare the DNA-cationic lipid reagent complexes.
5. Cell density should be between 50% to 80% confluency at the time of transfection (please refer to specific reagent manual for details). Cells should be in the mid-log growth phase. For better consistency and reproducibility of results between transfection experiments, accurately count your cells with either a hemocytometer or the Countess II FL Automated Cell Counter (Cat. No. AMQAF1000).
6. Confirm that the promoter and/or enhancer (any gene regulatory sequences) of the transfected DNA is compatible with the target cell type.
7. Do not use a cationic lipid reagent that has been frozen or stored at temperatures below 4 degrees C.
8. Include a positive control for the transfection assay (for example, Cat. No. A14146 for plasmid DNA transfection and Cat. No. 14750100 for siRNA transfection).

For additional tips ,please take a look at the tips outlined here (https://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-support/troubleshooting-transfection-experiments.html).

Find additional tips, troubleshooting help, and resources within our Lipid-Based Transfection Support Center.

What is the stability of your transfection reagents?

Our transfection reagents are shipped under ambient conditions and should be stored at 4 degrees C immediately upon receipt. We guarantee the performance of the product, if stored and handled properly, for one year from date of shipment unless otherwise stated on the tube label or COA. We do not recommend freezing transfection reagents, as this usually decreases transfection performance.

Please see this white paper (http://tools.thermofisher.com/content/sfs/brochures/cms_103226.pdf) on ambient shipping of Lipofectamine transfection reagents.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

I have tried several different transfection reagents and have failed to transfect my gene into my cell line of interest. Do you have any suggestions?

We recommend that you try electroporation as a method of delivering your plasmid of interest. We offer the Neon Transfection System for highly efficient transfection of primary cells, stem cells, and difficult-to-transfect cells. You may also consider using a viral-based system (https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-expression/mammalian-protein-expression/viral-delivery-mammalian-expression.html) to deliver your gene into your mammalian cell line of interest.

Find additional tips, troubleshooting help, and resources within ourTransfection Basics Support Center.

I see a small granular precipitate on my cells (microscopically) following addition of the transfection reagent:DNA complexes to my cells. Will it decrease the transfection efficiency?

It is normal to see some precipitate on the cells. However, a common reason for detecting unsually high precipitate on cells following lipid-based transfection is if there is excess EDTA or cationic lipid present. We recommend diluting the DNA in water or, if TE is preferred, use EDTA concentrations of <0.3 mM. Also ensure that concentrations of cationic lipid reagents do not exceed recommended amounts during complex formation. The presence or absence of this precipitate is not indicative of the transfection performance.

Find additional tips, troubleshooting help, and resources within ourTransfection Basics Support Center.

Why do I see cytotoxicity after performing transfection with Lipofectamine 2000? Can you please help?

Below are possible reasons why you may see reduced viability following transfection, along with suggested solution.

1. Possible Cause: DNA: transfection reagent ratio sub-optimal for cell line
   Suggested Solution: Prepare complexes using a DNA (µg) to Lipofectamine 2000 (µl) ratio of 1:2to 1:3 for most cell lines. Optimization may be necessary. If so, vary DNA (µg): Lipofectamine 2000 (µl) ratios from 1:0.5 to 1:5.
2. Possible Cause: Plasmid DNA preparation contains high levels of endotoxin
   Suggested Solution: Ensure that the plasmid DNA or siRNA used for transfection is of high quality. For plasmid DNA purification kits, we recommend using our PureLink HiPureNucleic Acid Purification Kits.
3. Possible Cause: Cell density was not optimal
   Suggested Solution: Lipofectamine 2000 works best in cultures that are >90% at the time of transfection.
4. Possible Cause: Complexes were added to cells in serum-free medium
   Suggested Solution: Try using growth medium containing serum when performing transfections. Transfection performance is typically better when the cells are more viable. If you require serum-free conditions, test medium for compatibility with Lipofectamine 2000 since some serum free formulations (e.g. CD293, SFM II, VP-SFM) may inhibit cationic lipid-mediated transfection.
5. Possible Cause: Complexes not thoroughly mixed in growth medium
   Suggested Solution: Following addition of transfection complexes into medium, ensure that the plate or wells are thoroughly mixed to prevent concentration of DNA:transfection reagent complexes in the wells
6. Possible Cause: Cells have changed over time, or splitting conditions have changed
   Suggested Solution: If transfection performance suddenly declines, it may be because of the cells. We recommend splitting and plating cells on a consistent schedule and in a manner where the cells are never too sparse or too dense. Excessive passaging also decreases transfection performance. If this is the case, start a new vial of cells from liquid nitrogen.
7. Possible Cause: Antibacterial agents were used in growth medium during transfection
   Suggested Solution: Do not use antibiotics such as chloroquine, penicillin, or streptomycin in growth medium because during transfection, cells are more permeable to antibiotics, which may cause toxicity.
8. Possible Cause: Transfection reagent stored improperly
   Suggested Solution: We recommend storing transfection reagents at 4°C. Freezing of transfection reagents, or storing them at room temperature, may decrease activity.
9. Possible Cause: Cationic lipid reagent was oxidized
   Suggested Solution: Do not vortex or agitate cationic lipid reagents excessively; this may form cationic lipid reagent peroxides.
10. Possible Cause: Selection antibiotic added too soon
    Suggested Solution: When creating stable cell lines, allow at least 72 hr for cells to express the resistance gene before adding selective antibiotic.

I am getting very low transfection efficiency with Lipofectamine 2000. Can you please provide some troubleshooting tips?

Below are possible reasons why you may be getting low transfection efficiency, along with suggested solutions:

1. Possible Cause: Plasmid DNA, siRNA, or transfection reagent diluted in media containing serum or complexes formed in the presence of serum
   Suggested Solution: Use serum-free medium for dilutions of plasmid DNA, siRNA, and transfection reagents. Note: we recommend using Opti-MEM | Reduced Serum Medium (Cat. No. 31985-062)to dilute Lipofectamine 2000 and DNA before complexing.
2. Possible Cause: DNA: transfection reagent ratio sub-optimal for cell line
   Suggested Solution: Prepare complexes using a DNA (µg) to Lipofectamine 2000 (µL) ratio of 1:2 to 1:3 for most cell lines. Optimization may be necessary. If so, vary DNA (µg): Lipofectamine2000 (µL) ratios from 1:0.5 to 1:5. If using a different transfection reagent, please consult the product manual.
3. Possible Cause: Not enough plasmid DNA used for dilution or complex formation
   Suggested Solution: Verify concentration using a second method or check the DNA for degradation. Determine DNA concentration by performing A260/A280 readings on a spectrophotometer or by using the Quant-iT DNA Assays Kits (Q33130, Q33120).
4. Possible Cause: Plasmid DNA or siRNA used in transfection has degraded or is of poor quality
   Suggested Solution: Ensure that the plasmid DNA or siRNA used for transfection is of high quality. For plasmid DNA purification kits, we recommend using our PureLink HiPure Nucleic Acid Purification Kits.
5. Possible Cause: Cell density was not optimal
   Suggested Solution: Lipofectamine 2000 works best in cultures that are >90% at the time of transfection.
6. Possible Cause: Complexes were added to cells in serum-free medium
   Suggested Solution: Try using growth medium containing serum when performing transfections. Transfection performance is typically better when the cells are more viable. If you require serum-free conditions, test medium for compatibility with Lipofectamine 2000 since some serum-free formulations (e.g. CD293, SFM II, VP-SFM) may inhibit cationic lipid-mediated transfection.
7. Possible Cause: Inhibitors were present in medium
   Suggested Solution: Do not use antibiotics, EDTA, citrate, phosphate, RPMI, chondroitin sulfate, hyaluronic acid, dextran sulfate, or other sulfated proteoglycans in the growth medium or in the medium used to prepare DNA:transfection reagent complexes.
8. Possible Cause: Problems with assay used to measure efficiency or expression
   Suggested Solution: Use a reporter gene to measure transfection efficiency. A reporter gene control allows you to confirm expression.
9. Possible Cause: Promoter-enhancer on vector is not recognized by the cell type
   Suggested Solution: Verify that the promoter-enhancer on your vector construct is compatible with the target cell type.
10. Possible Cause: Cells have changed over time, or splitting conditions have changed
    Suggested Solution: If transfection performance suddenly declines, it may be because of the cells. We recommend splitting and plating cells on a consistent schedule and in a manner where the cells are never too sparse or too dense. Excessive passaging also decreases transfection performance. If this is the case, start a new vial of cells from liquid nitrogen.
11. Possible Cause: Transfection reagent stored improperly
    Suggested Solution: We recommend storing transfection reagents at 4°C. Freezing of transfection reagents, or storing them at room temperature, may decrease activity.


Find additional tips, troubleshooting help, and resources within our Lipid-Based Transfection Support Center.

How do I perform a dose-response curve or kill curve?

The dose-response curve is a valuable tool to determine cell toxicity when exposed to various concentrations of antibiotic. The amount of selective antibiotic required to select for resistant cells varies with a number of factors, including cell type and type of antibiotic. We recommend performing a dose-response curve every time a new antibiotic (or a different brand) or a different cell line is used.

Experimental outline of dose-response curve assay:

1.Plate cells in a number of wells such that they are 25–30% confluent. This means that the cells are still dividing and hence will respond well to the antibiotic.
2.Dilute the antibiotic being tested to a broad linear concentration of the recommended range in growth medium.
3.Remove the growth medium from the cells. Apply the antibiotic-containing medium to the respective wells, leaving one set of wells empty. To these wells, add growth medium that does not contain the antibiotic.
4.Culture cells under proper growth conditions (change the medium every 3–4 days to get rid of dead cells and add fresh medium containing antibiotic) and observe the cells daily. At 10–14 days, assess the number of viable cells in each well. (This time period depends upon the antibiotic being tested; antibiotics such as Geneticin, Hygromycin, and Zeocin take about 3 weeks to kill cells, so waiting for 10–14 days would be ideal. However, for Blasticidin, which kills cells in about 2 weeks, waiting for 7–10 days would be sufficient.) To do this, aspirate the medium, wash the cells with phosphate-buffered saline and stain the cells with 0.5% methylene blue and 50% methanol for 20 minutes.
5.Plot the number of viable cells against the antibiotic concentration. This curve is the dose-response curve or kill curve. The lowest concentration of the antibiotic that kills all the cells in the chosen time period is then used for the stable selection.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What is the main advantage of viral transduction over transfection?

Transfection does not work for certain cell types such as non-dividing cells, whereas viral transduction works for dividing as well as non-dividing cells, such as neuronal cells that are hard to transfect.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What is the main advantage of lipid-mediated transfection over calcium phosphate-mediated transfection?

The main advantage of lipid-mediated transfection is the higher transfection efficiency that can be achieved with cell types that cannot be transfected using calcium phosphate. Calcium phosphate is prone to variability due to its sensitivity to slight changes in pH, temperature, and buffer salt concentrations. Calcium phosphate may also be cytotoxic to many cell types, especially primary cells. Further, lipid-mediated transfection can be used to deliver DNA ranging from oligos to large DNA, and can also deliver RNA and protein.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What is the main difference between transient and stable transfection?

During transient transfection the exogenous DNA does not integrate into the host genome, as a result some DNA is lost with every subsequent cell division. The expression is short-lived (maximum of 7-10 days) but the level of expression is high, since up to hundreds of copies of the DNA may be delivered into the cell. In stable transfection, under antibiotic selection pressure, the DNA integrates into the host cell genome and is passed onto their daughter cells during cell division. The expression is thus sustained as long as the selection pressure is maintained. The expression level is low since only 1-2 copies of the DNA may be integrated per cell. Transfection efficiency in a stable transfection is about 1-10% of that in a transient transfection.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

How do you estimate the amount of DNA using A260 readings? What does A260/A280 mean?

1 A260 unit (double stranded DNA in H2O) = 50 mg/mL. The extinction coefficient will change if DNA is diluted in a buffer other than H2O. This will change the value indicated above.

Sample calculation:

Volume of plasmid DNA sample = 100 mL

Dilution (1/20) = 25 mL of the sample in 475 mL H2O

A260 of diluted sample = 0.65

Note: For optimal results, make sure OD values are within 0.1 and 1.0.

Concentration of plasmid DNA sample = 0.65 x 50 mg/mL x 20 (dilution factor) = 650 mg/mL

Amount of plasmid DNA in sample = 650 mg/mL x 0.1 mL (sample volume) = 65 mg

An A260/A280 value that is between 1.8 and 2.0 means that the plasmid DNA is pure. A260/A280 readings that are less than 1.8 indicate that the sample may be contaminated with aromatic products (i.e., phenol) or protein. Readouts greater than 2.0 suggest that the sample is contaminated with RNA.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What are your recommendations with regards to endotoxin-free DNA for transfections?

For transfection-grade plasmid DNA, use either a PureLink HiPure or PureLink Expi Plasmid Purification Kit with plasmid purity equivalent to 2X CsCl gradients. For endotoxin-free DNA (< 9.1 EU/µg) use a PureLink Expi Endotoxin-Free Kit (Maxi, Mega, or Giga). Endotoxin-free DNA is recommended for sensitive applications such as transfection of primary cells and research on gene therapy for plasmid vaccines. For more information, please click here: http://www.thermofisher.com/us/en/home/brands/product-brand/purelink.html.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What types of molecules can be transfected using your lipid-based transfection reagents?

Our cationic lipid transfection reagents are used to transfect DNA (plasmids or oligonucleotides), siRNA (or miRNA), mRNA, or proteins. DNA delivered may be in the form of plasmids, cosmids, or even YAC clones as large as 600 Kb. Please refer to the Transfection reagent selection guide (http://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-reagent-application-table.html) to choose the best reagent based on cell type and application.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Can I use your lipid reagents to co-transfect plasmids?

Yes. The standard transfection protocol may be followed by keeping the total amount of DNA in the mixture constant. That is, if your protocol requires 1 µg plasmid, use 0.5 µg of each of two co-transfected plasmids, or 0.25 µg of each of 4 co-transfected plasmids. When performing co-transfections to introduce a selectable marker on a different plasmid, we recommend using a 3:1 to 10:1 molar excess of the plasmid of interest over the selectable plasmid to ensure that the plasmid of interest is present with the selectable plasmid.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Is there a place where I can find references from other researchers who have used your reagents?

Visit the product page for each reagent type and you will see a list of references at the bottom of the page. A table that lists specific cell line references is also accessible. We also recommend www.highwire.org as a search engine to find a large selection of up-to-date research articles using our transfection products. Simply include the name of the transfection reagent and your cell line/application of interest in your search criteria.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Where can I find cell line-specific transfection protocols?

Cell line-specific transfection protocols can be found here (http://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-support/transfection-selection-tool.html). If you do not find a cell line-specific protocol or if the transfection does not perform as expected, we recommend optimizing the conditions described in the product manual. Successful transfection depends on the cell type, amount of lipid, cell health, passage number, and cell density at the time of transfection. Each of these factors may differ slightly from lab to lab and may require additional optimization of the protocol to achieve the same result. Please review our helpful troubleshooting tips: https://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-support/troubleshooting-transfection-experiments.html. For more troubleshooting tips, please visit our Transfection Support Center (thermofisher.com/transfectionsupport).

Find additional tips, troubleshooting help, and resources within ourTransfection Basics Support Center.

Why would the expression level of my gene in transiently transfected cells be greater than those that are stably transfected?

Expression in transiently transfected clones is typically higher because transiently transfected cells can have up to hundreds of copies of the plasmid containing the gene of interest. Stably transfected clones usually harbor 1-2 copies integrated into the genome, and hence have lower levels of expression. Sometimes, the lower expression level in stably transfected cells is due to adverse effects of the recombinant protein on the cell when expressed constitutively.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Why are my transfections not reproducible?

In general, transfection efficiency will show some degree of variability between transfection experiments and among replicates in the same transfection experiment. For better reproducibility, keep all transfection parameters, such as cell confluency, passage number, and phase of growth, consistent between transfections. If possible, thaw fresh cells. We recommend preparing one master mix of the DNA/lipid complexes for the number of transfections planned to reduce multiple pipetting errors. When adding your complexes, we recommend changing tips between wells since re-used tips could bring carryover, especially for the 96- or 384-well format with small-volume formats. To further minimize the effects of transfection variability on data analysis, consider co-transfecting an internal normalization reference control such as beta-galactosidase or luciferase with the expression plasmid. Below are possible reasons for why your transfection results are not reproducible, along with suggested solutions:

1. Possible Cause: Cells have changed over time, or splitting conditions have changed
   Suggested Solution: If transfection performance suddenly declines, it may be because of the cells. We recommend splitting and plating cells on a consistent schedule and in a manner where the cells are never too sparse or too dense. Excessive passaging also decreases transfection performance. If this is the case, start a new vial of cells from liquid nitrogen.
2. Possible Cause: Transfections performed at different cell confluencies, or at different DNA:transfection reagent ratios
   Suggested Solution: Transfection performance reproducibility is dependent on day-to-day consistency in cell splitting, plating and transfecting with a consistent protocol (same DNA:transfection reagent ratios). Different DNA preparations or media changes may also change transfection performance.

I am working with well sizes different from those specified in your protocol. How do I scale up or scale down my transfection reaction?

Each of our transfection reagent protocols provides a table for scaling up or down transfections. Please consult the specific manual for details. For well or plates sizes not listed in the scaling table, calculate the total surface area and estimate the -fold difference from the 24-well. Use this -fold difference to adjust for reagent volumes, payload quantities, and seeding densities.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Can I use the same amount of any transfection reagent for different cell lines?

No.The transfection efficiency is highly dependent on the amount of reagent used per well and may be different between reagents. Please consult the product information that is provided with the transfection reagent for optimal use.

The protocol that is supplied with the product will provide you with an optimal range of transfection reagent to use per well. During product development, this range was determined to work well across a variety of cell lines. If you are still not achieving the performance you desire in your particular cell line, further optimization may be necessary. Please review our helpful troubleshooting tips: https://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-support/troubleshooting-transfection-experiments.html. For additional troubleshooting tips, please visit our Transfection Support Center (thermofisher.com/transfectionsupport)

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

Are cell density (% confluency) and passage number important considerations for transfection?

Yes, cell density is an important parameter in influencing transfection efficiency. If the seeding density is too low, some cytoxicity may be observed. If the cell density is high, lower than expected transfection efficiency may be observed. Both issues may be easily resolved by either descreasing or increasing the quantity of complexes added to the culture. We recommend using Lipofectamine 3000 since it shows the best flexibility for variable seeding density without showing cytotoxicity issues and maintains high protein expression. Lipofectamine 3000, Lipofectamine 2000, and Lipofectamine LTX/PLUS provide excellent transfection efficiencies at confluencies between 70 and 90%. Some toxicity may be observed at lower confluencies but may be alleviated by decreasing quantity of complexes or removing the complexes after 4-6 hours incubation and refreshing the media. Lipofectamine RNAiMAX works best at confluencies between 60 and 80%.

Passage number may affect transfection experiments. We recommend consistent splitting and plating of cells. Excessive numbers of passages may decrease transfection performance. We do not recommend splitting cells for more than 20-30 passages. If transfection performance declines and cells have been in culture for a long time or excessively/improperly passaged, we recommend that you restart your cultures with a new vial of cells from liquid nitrogen. Please refer to the Gibco Cell Culture Basics handbook (https://www.thermofisher.com/us/en/home/references/gibco-cell-culture-basics.html) for proper guidelines for culturing and passaging cells.

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What recommendations do you have for selecting a transfection reagent?

Choose the best reagent by cell type and application by using the Transfection reagent selection guide (http://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-reagent-application-table.html).

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

What are the different methods available for transfection?

There are many transfection methods available to deliver plasmids, DNA fragments, oligos, siRNAs, mRNA, or proteins for a wide range of research and drug discovery applications. A review of the pros and cons of each technique is provided here (https://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection-support/gene-delivery-selection-guide.html).

Find additional tips, troubleshooting help, and resources within our Transfection Support Center.

My ExpiFectamine 293 Transfection Kit (Catalog No. A14525) was accidentally frozen. Can I still use it?

ExpiFectamine reagents generally does not transfect well after being frozen, as the freezing disrupts the lipid micelles. Therefore, we do not recommend using this kit.

Find additional tips, troubleshooting help, and resources within our Transfection Basics Support Center.

What method do you recommend for quantifying rabbit IgG expression from pRABBIT IgG IRES-EmGFP Positive Control Vector, Cat. No. A39243?

The formation of intact IgG molecules may be quantified using a sandwich ELISA designed to capture and detect rabbit IgG. Besides the rabbit IgG positive control vector, reagents, and consumables that are included in the kit, you will also need purified rabbit IgG to be used as a standard, F(ab')2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, HRP (Cat. No. A10547), Protein A Coated Plates, Clear, 96-Well (Cat. No. 15130), TMB Substrate Kit (Cat. No. 34021), SuperBlock (TBS) Blocking Buffer (Cat. No. 37535), and PBS or TBS buffer for washes. There is an example procedure in our Protein A Coated Plates manual (https://tools.thermofisher.com/content/sfs/manuals/MAN0011310_Thermo Scientific_ProteinA_G_AG_Coat_96Well_UG.pdf). Please note that our R&D scientists determine titer values from crude cell culture supernatants using a Pall Life Sciences FortéBio Octet instrument equipped with a Protein A biosensor.

Find additional tips, troubleshooting help, and resources within our Protein Expression Support Center.

Do you offer a GFP-expressing mammalian expression vector that I can use as a control to monitor my transfection and expression with the Expi systems?

We offer pRABBIT IgG IRES-EmGFP Positive Control Vector, Cat. No. A39243, which you can use to monitor your transfection and expression.

Find additional tips, troubleshooting help, and resources within our Protein Expression Support Center.

Do I need to change media after transfection in the Expi293 Expression System?

No. The Expi293 Expression System is designed to run without media changes. There is no need to remove transfection complexes or to change growth medium following transfection.

Find additional tips, troubleshooting help, and resources within our Protein Expression Support Center.

I only added one enhancer and not the other with the Expi293 system. Will I still get good protein expression?

The Enhancers are designed to work together for maximal expression. Addition of just one Enhancer will result in reduced expression and may be anywhere from one third to two thirds the level of expression obtained if both Enhancers had been added on time.

Find additional tips, troubleshooting help, and resources within our Protein Expression Support Center.

What method do you recommend for quantifying the rabbit Antibody-Expressing Positive Control Vector (Cat. No. A14662)?

The formation of intact IgG molecules may be quantitated using a sandwich ELISA designed to capture and detect rabbit IgG. Besides the rabbit IgG positive control, reagents, and consumables that are included in the kit, you will also need purified rabbit IgG to be used as a standard, F(ab')2 goat anti-rabbit IgG HRP conjugate (Cat. No. A10547), Protein A-coated plates (Cat. No. 15130 for clear plates used in colorimetric detection), TMB colorimetric substrate (Cat. No. 34021), SuperBlock (TBS) Blocking Buffer (Cat. No. 37581), and PBS or TBS buffer for washes. There is an example procedure in our Protein A-coated plates manual (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0011310_Pierce_ProteinA_G_AG_Coat_96Well_UG.pdf). Please note, our R&D scientists determine titer values from crude cell culture supernatants using a Pall Life Sciences FortéBio Octet instrument equipped with a protein A biosensor.

Find additional tips, troubleshooting help, and resources within our Protein Expression Support Center.