Automated Tissue Culture Cell Fixation and Staining in Microplates

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Invited-icon.jpgA LabAutopedia invited article

Authored by: Paul Held, Bridget Bishop, Peter Banks, BioTek Instruments, Inc.

Originally published as a white paper by BioTek Instruments, Inc., April 15, 2013.  Reprinted with permission.

Using the EL406™ Combination Washer Dispenser to Prepare Samples for Imaging with the Cytation™3 Cell Imaging Multi-Mode Reader



Fluorescence microscopy has traditionally been performed on microscope slides, but there is a growing trend towards the use of 96- and 384-well microplates as this allows greater number of samples to be easily processed and automated. This is certainly true in the field of High Content Screening. Here we describe the use of the EL406™ Combination Washer Dispenser to automate the fixation and staining processes typically used prior to fluorescence imaging.


The hallmark of fluorescent microscopy is the use of specific mouse monoclonal antibodies to recognize and bind to cellular structures. The antibody is a marvelous tool of remarkable selectivity. It can be used to identify and quantify almost any protein in complex biological matrices. Its use as a fluorescent marker in microscopy dates back to the pioneering work of Albert Coons directly after World War II, where with colleagues, he labeled antipneumococcus antibodies with anthracene isocyanate and thereby made an antibody that could fluoresce under UV light. Today there are myriad fluorescent probes that emit across the visible to near IR spectrum and can be used to make fluorescent antibodies. While occasionally primary antibodies are directly labeled, more often a labeled secondary antibody that recognizes the species and the type of the primary antibody is used to visualize the structure. The size of the primary antibody also allows the binding of multiple copies of the secondary antibody, whereas the original target epitope may not, providing a means to amplify the signal. Antibodies are large macromolar proteins which are not cell membrane permeable, thus for fluorescence microscopy applications the cells must be fixed and/or permeabilized, typically using formalin or methanol and a detergent. This allows antibodies to access the various organelles and their proteins which are of interest.

Alterations in cellular morphology can often be followed through the use of actin-specific stains, such as Alexa Fluor® 488-phalloidin. Phalloidin is a bicyclic peptide toxin associated with death cap Amanita phalloides mushrooms that specifically binds to cellular actin polymers, while the covalently attached Alexa Fluor 488 moiety allows for fluorescent visualization.

Phalloidin binds to actin at the junction between subunits; and because this is not a site at which many actin-binding proteins bind, most of the F-actin in cells is available for phalloidin labeling[1]. Because fluorescent phalloidin conjugates are not permeant to most live cells, like antibodies, they require that cells be either fixed and/or permeablized. Labeled phalloidins have similar affinity for both large and small filaments and bind in a stoichiometric ratio of about one phalloidin molecule per actin subunit. Phalloidins have some advantages over antibodies for actin labeling. Their binding properties do not change appreciably with actin from different species, including plants and animals. In addition, their nonspecific staining is negligible and unlike some antibodies they only bind filament polymers, resulting in good contrast between stained and unstained areas. Because cellular actin polymers serve as cytoskeletal elements fluorescent stains that bind them can be used to identify cellular cytoplasmic regions.

DAPI (4', 6-diamidino-2-phenylindole) is a fluorescent stain that binds strongly to A-T rich regions in DNA. As such, this stain is specific for the nuclear regions of the cell, with minor staining of the mitochondrial DNA. DAPI has the ability to pass through intact cell membranes, so it can be used to stain both live and fixed cells, though it passes through the membrane less efficiently in live cells and therefore the effectiveness of the stain is lower. When bound to double-stranded DNA, DAPI has an absorption maximum at a wavelength of 358 nm and its emission maximum is at 461 nm. Due to its ability to fluorescently stain DNA, it is a very popular marker for cell nuclei.

Regardless of the antibody and fluorescent dye combination used in fluorescence microscopy using microplates, a series of aqueous reagent additions and wash steps to remove unbound materials is required for fixing and specific staining with low background. Here we describe the use of the EL406 Combination Washer Dispenser from BioTek Instruments to automate the reagent additions, as well as the wash steps necessary for the preparation of cell samples in 96- and 384-well plates prior to analysis in the Cytation™3 Cell Imaging Multi-Mode Reader. Figure 1 demonstrates a 3-color stain image of U-2 OS cells using the EL406 Combination Washer Dispenser.

Figure 1. Three color staining of a monolayer of U-2 OS cells in a 96-well plate. Nuclei were stained with DAPI; F-actin stained with Alexa Fluor 488-phalloidin; and an antimitophillin antibody labeled with Texas Red. The obvious yellow coloring is produced by the superposition of Alexa Fluor 488 and Texas Red dyes. Scale bar indicates 80 μm.

Materials and Methods


NIH3T3, HEK293 and U-2 OS cells were grown in Advanced DMEM (cat # 12491) from Life Technologies supplemented with 10% FBS, 2mM glutamine. Black sided, clear bottom 96-well (cat # 3603) and 384-well (cat # 3712) were from Corning. TopSeal-A (cat # 6050195) adhesive plate sealers were from PerkinElmer. DAPI dihydrochloride stain (cat # D1306), Alexa Fluor 488 phalloidin (cat # A12379), Texas red phalloidin (cat # 7471) anti-mitofilin monoclonal antibody (cat # 456400), Texas red goat anti-mouse IgG (cat # T862) and DPBS (cat # 14190), were obtained from Life Technologies. Paraformadehyde (cat # P6148) powder was obtained from Sigma-Aldrich, while Triton X-100 (cat # X198-05) was from Baker.


Liquid Handling

All cell washes and reagent additions for cell fixation, permeabilization and fluorescent staining were carried out using the EL406 Combination Washer Dispenser. The EL406 provides full plate washing along with three reagent dispensers in one, compact instrument. Both peristaltic pump and syringe pump dispensers were used. For expensive biological reagents, such as primary and secondary antibodies, the peristaltic pump dispenser is optimum as unused portions of the reagent can be easily retrieved; for inexpensive chemical reagents such as fixatives and detergents used to permeabalize cells, syringe pumps can be used. In order to maintain sterility, the EL406 Washer Dispenser was placed in a biosafety cabinet and 5 μL cassettes for the peristaltic pump were sterilized by autoclaving prior to use.

Cell Imaging

Cells were imaged using an Cytation3 Microplate Imager (BioTek Instruments, Winooski, VT) configured with DAPI, GFP and Texas Red light cubes. The imager uses a combination of LED light sources in conjunction with band pass filters and dichroic mirrors to provide appropriate wavelength light. The DAPI light cube is configured with a 377/50 excitation filter and a 447/60 emission filter; the GFP light cube uses a 469/35 excitation filter and a 525/39 emission filter; while the Texas Red light cube uses a 586/15 excitation and 647/57 emission filters.

Fixed Cell Imaging Processes


Cells were washed once with 200 μL of DPBS (NaCl 137 mM, KCl 2.7 mM, Na2HPO4 10 mM, KH2PO4 7.4 mM) prior to fixation using the EL406 washer manifold. After which 100 μL of 4% paraformaldehyde (PFA) solution was added using the EL406 syringe pump dispenser manifold. PFA solution was made daily by dissolving 4 g of powder into 100 mL of DPBS warmed to 60 °C. Cells were fixed for 10 minutes at room temperature followed by 2 washes of 200 μL using DPBS.

DAPI Staining

Following the fixation process described above, cells were permeablized for 10 minutes using 50 μL of DPBS containing 0.1% Triton X-100 added with the syringe pump dispenser. Cell nuclei were then stained with 50 μL of working solution of DAPI. Working DAPI solution was prepared from a 14.3 mM stock by dilution to 30 μM in DPBS+0.1% Triton X-100. Cells were stained 10 minutes at room temperature followed by 2 washes with 200 μL of DPBS. After aspiration 100 μL of DPBS was added to all wells and the plates sealed using an optically clear TopSeal-A adhesive plate sealer (Perkin Elmer). Prepared plates were kept at room temperature and protected from light prior to imaging.

Two Color Staining: Phalloidin and DAPI

Following the fixation and permeabilization processes described above, Cellular actin was then stained using 50 μL of a working solution of either Alexa Fluor 488 or Texas Red phalloidin. Alexa Fluor 488 phalloidin working solution was prepared fresh by dilution of 6.6 μM mM stock methanol solution to 30 nM in DPBS. The stock solution was stored at -20 °C until needed. Cells were stained for 10 minutes followed by a one-cycle wash with 200 μL of PBS 0.1% DAPI Staining could then be performed according to the process described above.

Three Color Staining: Antibody, Phalloidin and DAPI

Cells were fixed and permeabilized according to the processes described above. Then, using the peripump dispenser, 50 μL of primary mouse monoclonal antibody (1:750) dilution in DPBS, 30 mg/mL BSA, 0.1% Triton X-100) specific for mitochondrial protein mitofilin was added and the plate incubated at room temperature for 60 minutes. The plate was washed one time with DPBS 0.1% Triton X-100 and the secondary Texas Red labeled fluorescent anti- mouse IgG antibody (1:500 dilution in PBS, 30 mg/mL BSA, 0.1% Triton X-100) was added and allowed to incubate for 60 minutes at room temperature followed by a wash with DPBS 0.1% Triton X-100. Following antibody staining, phalloidin, then DAPI staining were performed according to the processes described above and evident in the work flow contained in Figure 2.

Figure 2. Automated Workflow for Cell Seeding, Fixation, Permeabilization and Three Color Staining Process. An EL406 Combination Washer Dispenser controlled by Liquid Handling Control (LHC) software was used to carry out the process steps for cell fixation, permeabilization and staining with three colors: DAPI nuclear stain, Alexa-Fluor 488 phalloidin actin stain and Texas red labeled secondary antibody.

Table 1. EL406 Combination Washer Dispenser pump usage for staining processes.

Table 2. EL406 Combination Washer Dispenser parameters.


Fixation and DAPI Staining of Cells

Cellular expression of transiently transfected genes is a very common experimental procedure. Many of these expression experiments use easily traceable genetic elements (e.g. GFP) either as a direct reporter for assessment of gene expression or as an internal control for transfection efficiency. Direct single color image analysis can be used to identify numbers of positively expressing cells (Figure 3). Alternatively, two color blue, green analyses can be used where the nuclei specific blue-DAPI stain can be used to identify all cells, while the green GFP specific color is used to identify the positively expressing cells. In either case cell fixation can be used to prevent alterations that may occur during the image capture process.

Figure 3. GFP expressing NIH 3T3 cells fixed with 4% Para-formaldehyde and stained with DAPI. Image represents an overlay composite of brightfield, and both blue and green fluorescence. Scale bar indicates the size of 80 μm.

As demonstrated in Figure 3, GFP expressing cells can be fixed with 4% PFA using the EL406 and GFP fluorescence detected. In this image a manual count of the cells indicates approximately 25% of the cells are positive for GFP expression. It is important to note that fluorescent proteins require hydration so fixation using cold methanol often leads a loss of fluorescence. Image analysis that automatically calculates transfection efficiency often requires that all cells be identified in some fashion. Nuclear stains, such as DAPI, work well to identify total cell number, while analysis of GFP signals identifies positive cells. The ratio of the two values is the transfection efficiency.

Figure 4 demonstrates that the EL406 can fix cells and then add DAPI stain. HeLa cells were first fixed with 4% PFA. During the 10-min incubation, the peripump was used and DAPI stain added. Manual cell counting indicates that 43% of the total cells are positive for GFP expression.

Figure 4. NIH3T3 cells transfected with GFP. Cells in 96-well plates were fixed with PFA and stained with DAPI. Image represents an overlay composite of green and blue fluorescence. Scale bar is 80 μm in length.

Two Color Staining of Cells

Non-fluorescent cells can also be stained with two different fluorescent stains after fixation. Usually, this requires permeabilization of the cell, as is the case here with the use of phalloidin. PFA fixed cells can be stained with both Texas red-phalloidin and DAPI in succession. Peripump cassettes were swapped between reagent additions such that a fresh cassette was used for each reagent addition. In Figure 5, all cells have been stained with both an actin specific stain as well as a DNA specific stain.

Figure 5. Fixed U-2 OS cells in 96-well microplates stained for F-actin and DNA. F-actin was stained with Texas Red phalloidin, nuclear DNA was identified with DAPI. Image represents the overlay of separately captured blue and green fluorescent signals. Scale bar represents 80 μM.

GFP expressing cells can be stained with fluorescent dyes that do not overlap the fluorescent protein's spectrum. Cells treated with DAPI and Texas redphalloidin will result in a three color fluorescent image depicted in Figure 6. Red staining identifies F-actin filaments and cellular attachment points, while the green signal denotes GFP located primarily in the cytoplasm and the blue DAPI signal identifies the nucleus. Note that the GFP signal will often fade much quicker than the small molecule fluorescent compounds such as DAPI, Texas red or Alexa Fluor 488 often used. In addition fluorescent proteins require hydration in order to be fluorescent, which rules out the use of methanol as a fixative agent.

Figure 6. NIH 3T3 cells expressing GFP. F-actin was stained with Texas Red-phalloidin and nuclear DNA was identified with DAPI. Image represents the overlay of separately captured red, blue, and green fluorescent signals. Scale bar represents 80 μm.

Three Color Staining of Cells

The sequential addition of multiple stains, each specific for a separate cellular target and with a distinguishable signal is a commonly used fluorescence microscopy technique. One is only limited by the ability to identify specific targets and the capability of the imaging instrument being used. Figures 7 demonstrates the ability of the EL406 to fix and permeabalize U-2 OS cells and then add a primary antibody specific to mitochondrial proteins, along with a fluorescent labeled secondary detection antibody that recognizes the primary antibody and two other stains. In this three-color image mitochondria are identified by the red signal, cytoplasmic F-actin identified by green and nuclei by blue signals.

Figure 7. U-2 OS cells stained for mitochondria, F-actin and nucleus. Cells in 96-well plates were fixed and stained for mitochondria (Texas Red), F-actin (Alexa Fluor 488), and DNA (DAPI). Scale bar indicates 80 μm.

Higher density plates are being used more often in conjunction with high content screening. The EL406 is capable of processing 96- and 384-well plates without changing manifolds. As demonstrated in Figure 8, HeLa cells expressing GFP cultured in 384-well microplates can be fixed and washed using the EL406. Cell monolayers were intact and cells uniformly fluorescent.

Figure 8. HeLa-GFP cells in 384-well microplates fixed with 4% PFA. Scale bar indicates 1000 μm.

Likewise, cells can be stained with DAPI. As shown in Figure 9, NIH3T3 cells show uniform staining for nuclei.

Figure 9. NIH3T3 cells expressing GFP in 384-well microplates. Cells were fixed with 4% PFA, and stained with DAPI. Scale bar indicates 400 μm.


These image data indicate that the EL406 Combination Washer Dispenser can be used to automate the cell fixation, permeabilization and staining processes used in many fluorescence microscopy experiments using microplates, including High Content Screening (HCS). Automation of the sample preparation steps of these experiments allows for a significant increase in the numbers of samples that can be analyzed. In addition, automation provides a level of consistency not seen with manual processing.

Most staining procedures require that the cells be permeablized with some sort of detergent, such as Triton X-100. Large molecules such as antibodies and phalloidins will not cross intact membranes. While DAPI is reported to cross membranes and work on nonpermeablized cells, it does so much less efficiently than cells that have been permeablized. We routinely use Triton X-100 with DAPI staining to insure adequate stain penetration. Because of their high specificity, brightness, physical robustness and large amount of target, phalloidin and DAPI staining can often be combined into a single step, saving time and subjecting the cells to less washing.

The numerous process steps required to fluorescently stain cells with three colors can be modified extensively depending on the needs of the researcher. Many experimental questions do not require three color staining. For example, measuring transfection efficiency of GFP expressing cells may only require a DAPI fluorescent stain, after fixation with 4% PFA.

Positive cells will produce green fluorescence, while all cell nuclei will be stained blue with DAPI. Alternatively, cell morphology can be identified with fluorescent phalloidin stains specific to actin and DAPI stain will identify nuclei. Nuclear translocation assays need only have a stain identifying the protein in question and DAPI to identify the nucleus of the cell. The individual process steps can be used or not used as experimentally needed. At the end of the required process, a final wash to remove unbound stain or antibodies followed by the addition of PBS to keep the samples hydrated is all that is necessary.

The EL406 Combination Washer Dispenser has a number of features that make it amenable for the process steps of fixing and staining tissue culture cells prior to fluorescence microscopy. Typically cells are washed with PBS or similar isotonic buffer between reagent additions to remove unwanted media or to eliminate unbound antibodies or dyes. The washer manifold has a full 96 head that is capable of rapidly washing either 96- or 384-well microplates without changing washer manifolds. In addition, the combination of syringe pump and peripump dispensers allows for the addition of different reagents. Use of the peripump dispenser (Table 1) in conjunction with a 1 μL cassette allows the user to minimize the amount of overage required for an adequate dispense. Unused precious reagent can also be recovered by reversing the peripump and purging the lines back into the reagent container. Additionally, the multiple reagent paths of the peripump can be used to add different antibodies or stains to different wells on the same microplate; thus allowing for side by side comparisons without the need for subsequent reagent additions. The syringe pumps allow for different reagents (e.g. PFA fixative and permeabilization buffer) to be added using separate fluid paths without any manual intervention.

Automation of the staining process steps requires the ability to gently add and remove fluids from microplate wells without physically damaging the cells in the wells. As described previously physical trauma to cells can result from using too vigorous of a dispense rate[2]. This is particularly true of the wash buffer being dispensed from 96-tubes simultaneously. Leaving a fluid residual serves to minimize the impact of incoming washer buffer. The residual used needs to be balanced with the dilution to any subsequent reagent added. Towards that end we used physical offsets to move the dispense tubes for the washer manifold to one edge of the wells (Table 2). Likewise having the aspiration tubes in close contact with the cell layer for an extended period of time is harmful to the cell monolayer. A small yet strong vortex occurs near the aspiration tube that can damage fixed or live cells. The use of rapid aspiration dive rates minimizes the exposure of cells to this deleterious force (Table 2).

HCS has started to play a significant role in the drug discovery process, beyond secondary screening. By marrying the wealth of information accessible through microscopy with large numbers of experimental conditions in a single experiment, unique pieces of information can be gathered that might have been missed with either a traditional cell based screen or a manual microscopic study. Microscopic image based analysis often requires significant amount of manual sample processing, which can be tedious and subject to process errors that can result in artifacts. The use of automation for these steps, besides being faster also eliminates any technician bias of the data.

Alexa Fluor® is a registered trademark of Molecular Probes Inc.


  1. Steinmetz, M. O., Stoffler, D., Müller, S. A., Jahn, W., Wolpensinger, B., Goldie, K. N., Engel, A., Faulstich, H. & Aebi, U. Evaluating atomic models of F-actin with an undecagold-tagged phalloidin derivative. J Mol Biol. 1998, 276,1-6.
  2. Held. P. BioTek Application Note (2005)

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