How To Use A Cell Strainer?

Preparing a high-quality cell suspension is important for many laboratory applications. Cell suspensions may contain tissue debris, large particles, or cell aggregates, which can affect downstream experiments. A cell strainer uses a mesh with a defined pore size to remove unwanted larger materials and help produce a more uniform cell suspension. It is commonly used before cell counting, cell culture, flow cytometry, and other cell-based analyses. Proper use is important to reduce clogging, cell loss, and cell damage. This article explains how to use a cell strainer step by step, as well as common problems and practical precautions.

What Is a Cell Strainer?

A cell strainer, also known as a cell filter or cell sieve, is a tool used to isolate primary cells from tissues and remove cell clumps and impurities. By precisely controlling pore size, it allows for the separation of different cell types, providing high-quality single-cell suspensions for downstream experiments such as flow cytometry and single-cell sequencing. The pore size of a filter is generally expressed in mesh size. A higher mesh size indicates a smaller pore size, resulting in finer particles filtered. Its emergence has transformed cell separation procedures from the cumbersome gauze filtration era into a more standardized and efficient one.

Based on usage scenarios and requirements, cell filters are primarily categorized as follows:

By Material: Most are disposable, sterile plastic mesh screens, typically made from polymers such as polycarbonate or polyester. These materials offer excellent chemical resistance and durability, ensuring experimental stability and reproducibility.

By Pore Size (Mesh): This is the most critical categorization, with different mesh sizes corresponding to different applications:

• 40 micron cell strainer (375 mesh): High-precision filtration of small cells (such as stem cells and CTCs), removing impurities ≥20μm, suitable for flow cytometry and single-cell sequencing.
• 70um cell strainer (210 mesh): A general-purpose separation tool that balances efficiency and purity, suitable for tumor cell and primary cell isolation and routine culture experiments.
• 100 um cell strainer (150 mesh): Rapidly pre-processes tough tissues (such as tumors, liver, and lung), removing tissue fragments ≥100μm to protect downstream experiments.

Why Use a Cell Strainer?

Removing Tissue Debris: During tissue dissociation, incomplete mechanical or enzymatic digestion may leave behind tissue fragments and other large particles. These materials can interfere with cell counting, sample handling, and downstream analysis. Filtering the suspension through a cell strainer helps remove larger debris and improves the overall uniformity of the sample.

Reducing Cell Clumps: Cells may form aggregates during tissue dissociation, cell harvesting, or suspension preparation. Large cell clumps can make cell counting less accurate and may interfere with downstream procedures. A cell strainer can help remove larger aggregates and improve suspension consistency.

Improving Cell Suspension Uniformity: A more uniform cell suspension is generally easier to handle and distribute into different experimental vessels. Filtration can reduce the presence of large particles and aggregates, helping produce a more consistent sample.

Preparing Samples for Downstream Applications: Cell strainers are commonly used before procedures that require a relatively uniform cell suspension, including: cell counting; cell culture; flow cytometry; cell sorting; single-cell analysis; other cell-based assays. 

How To Use a Cell Strainer？

Step 1: Prepare the Cell Suspension

Before filtration, prepare the cell suspension according to the experimental protocol. For tissue-derived samples, complete tissue dissociation as much as possible before filtration. If large tissue fragments or cell aggregates are visible, gently pipette or use an appropriate dissociation method to reduce their size. Avoid excessive mechanical force, which may affect cell viability. The suspension should be as uniform as possible before filtration to reduce the risk of clogging.

Step 2: Prepare the Cell Strainer and Collection Tube

Place the cell strainer securely on a compatible collection tube or receiving vessel. Make sure the strainer is stable before adding the sample. For sterile applications, use sterile cell strainers, collection tubes, and other necessary accessories, and follow appropriate aseptic procedures. Before use, check the strainer to make sure the mesh is intact and free from visible contamination or damage.

Step 3: Add the Cell Suspension

Gently transfer the cell suspension onto the cell strainer. It is generally better to add the sample gradually rather than all at once. For samples with a high concentration of cells or debris, divide the suspension into several portions. Allow each portion to pass through before adding more. Avoid dispensing the sample forcefully onto the mesh, as excessive mechanical force may increase cell stress.

Step 4: Allow the Suspension to Pass Through the Strainer

Allow the suspension to pass through the mesh naturally. The cell strainer retains larger tissue fragments, cell aggregates, and other particles while allowing smaller components to pass through. If filtration becomes significantly slower, stop adding sample and check whether the strainer is overloaded or clogged. Avoid forcing a clogged strainer, as excessive pressure may damage cells or allow unwanted particles to pass through the mesh.

Step 5: Rinse the Cell Strainer if Necessary

If required by the experimental protocol, gently rinse the cell strainer with an appropriate buffer or culture medium after filtration. Rinsing can help recover cells remaining on the mesh. However, excessive rinsing may dilute the cell suspension, so the rinsing volume should be appropriate for the downstream application.

Step 6: Collect the Filtered Cell Suspension

After filtration, carefully remove the cell strainer and collect the filtered cell suspension from the receiving tube. Depending on the experimental workflow, the filtered suspension can be used directly or further processed by cell counting, centrifugation, washing, resuspension, or other procedures. If cell viability is important, process the filtered suspension promptly according to the requirements of the specific experiment.

Common Problems When Using a Cell Strainer

Why Does the Cell Strainer Clog?

Clogging may occur when the sample contains too much undigested tissue, excessive debris, or large cell aggregates. Adding too much sample at one time may also contribute to blockage. To reduce clogging, prepare the sample adequately before filtration and add the suspension gradually.

Why Is Filtration Too Slow?

Slow filtration is often associated with partial blockage of the mesh or a sample containing a high concentration of debris or aggregates. Avoid applying excessive pressure. Instead, check the sample condition and consider whether further sample preparation is needed.

Why Are Cell Clumps Still Present After Filtration?

If cell aggregates remain after filtration, the clumps may be small enough to pass through the mesh or may have formed again after filtration. Gentle handling, proper sample preparation, and appropriate processing conditions can help reduce aggregation.

Why Is Cell Recovery Low?

Low cell recovery may result from excessive retention of cells on the strainer, incomplete sample transfer, or unnecessary cell loss during handling. Using an appropriate rinsing procedure, minimizing unnecessary transfers, and avoiding excessive mechanical force may help improve recovery.

Tips for Better Cell Recovery and Filtration Performance

Prepare the Sample Before Filtration: Proper sample preparation can reduce the amount of large debris and aggregates reaching the strainer, helping maintain smoother filtration.

Add the Sample Gradually: Adding the suspension in smaller portions can reduce sudden accumulation of material on the mesh and help prevent clogging.

Avoid Excessive Mechanical Force: Do not force a heavily blocked sample through the strainer. Excessive mechanical force may damage cells or negatively affect cell viability.

Rinse When Appropriate: A gentle rinse may help recover cells remaining on the strainer. However, excessive rinsing may dilute the sample unnecessarily.

Minimize Unnecessary Handling: Each additional transfer or handling step may increase the possibility of cell loss. Keeping the workflow simple and efficient can help improve overall sample recovery.