Mouse Immune Cell Isolation
Streamline Your Mouse Research Workflow with EasySep™
As mouse research evolves and experimental models become more specialized, every sample matters more than ever. EasySep™ Mouse Cell Isolation kits help you recover high-quality cells from a wide range of tissues and models, including complex and humanized systems, while preserving cell phenotype and function. By minimizing cell loss and standardizing key steps, EasySep™ supports consistent, reproducible, and scalable performance across experiments and users. Whether you're working with limited tissue, transitioning to advanced models, or optimizing workflows for efficiency, EasySep™ enables reliable cell isolation for downstream applications such as flow cytometry, cell culture, and molecular analysis.
Why Use EasySep™ for Mouse Cell Isolation?
- Simplify mouse cell isolation with fewer processing steps, in as little as 15 minutes.
- Achieve up to 99% cell purities with high recoveries.
- Obtain viable, functional cells without the need for columns and washes.
- Isolate cells from a wide range of mouse tissues, including spleen, blood, bone marrow, and more.
- Widely used in published research for over 20 years, supporting diverse downstream applications.
Cell Isolation Methods
Several cell isolation methods are available for mouse research, each suited to different cell populations, sample types, and downstream applications. EasySep™ uses magnetic cell separation to simplify how you isolate mouse cells from a variety of samples. Antibody complexes bind to specific cell surface markers, linking selected cells to magnetic particles. When the sample is placed in an EasySep™ magnet, labeled cells are separated, allowing you to easily isolate your target population or remove unwanted cells. This approach reduces workflow complexity and enables efficient processing of a wide range of mouse tissues, including spleen, lymph node, bone marrow, tumor samples, and more.
How Magnetic Cell Separation Supports Mouse Cell Isolation
- Preserves native cell characteristics for downstream functional and phenotypic analysis
- Adapts to diverse mouse models, including humanized systems
- Supports multiple isolation strategies, including:
- Negative cell isolation
- Positive selection
- Customizable workflows for specialized applications
When to Use Positive vs. Negative Cell Isolation
Positive and negative selection methods serve different purposes in mouse cell isolation workflows. Negative selection is commonly used to isolate untouched cells for functional assays. In contrast, positive selection directly labels and isolates target cells, making it useful when high purity or specific cell capture is required. The choice depends on your downstream application, sample type, and experimental goals. If you need help deciding, contact us at techsupport@stemcell.com.
Why Use Negative Selection for Mouse Cell Isolation?
Negative selection is widely used in mouse cell isolation workflows when maintaining native cell characteristics is critical. Instead of labeling target cells, unwanted cells are removed using antibody complexes and magnetic particles, allowing you to isolate untouched cells in their natural state.
We use EasySep™ (CD4+ and CD8+ T cell negative selection kits, as well as the Mouse B Cell Isolation Kit, and the Mouse Pan-DC Enrichment Kit) because of its ease of use and the high purity that we get from the preparation. I especially like the negative selection kits because it allows us to keep the cells that we collect as undisturbed as possible.
Eric, MD/PhD Student, Yale University
This approach is particularly valuable for applications that rely on functional and phenotypic accuracy, including immune assays, cell culture, and translational studies using complex or humanized mouse models. Negative selection also helps preserve cell surface markers for immunophenotyping and supports RNA integrity for downstream transcriptomic analysis.
Figure 1. Typical EasySep™ Mouse Cell Isolation Protocol (Negative Selection)
EasySep™ negative selection kits enable isolation of untouched mouse cells, including B cells, T cells, and NK cells, ready for immediate downstream use. Explore our full range of negative cell isolation kits.
Compare Mouse Cell Isolation Methods
If you’re comparing approaches or optimizing your workflow, these resources can help:
Magnetic Cell Separation vs. Other Methods
Compare magnetic separation with alternative cell isolation techniques.
EasySep™ Frequently Asked Questions (FAQs)
Learn about EasySep™ cell isolation, product compatibility, sample requests, and more.
Performance Data: Cell Purity & Recovery
EasySep™ mouse cell isolation kits simplify mouse cell isolation workflows with rapid processing, ensuring high cell purity and recovery across diverse mouse cell types and tissues. Additionally, EasySep™ technology is column-free, reducing mechanical stress on cells while preserving cell functionality and maximizing yield. EasySep™ delivers high-purity results with equivalent or improved purity and recovery compared to column-based cell isolation methods. The examples below highlight typical isolation times, purity profiles, and comparative performance across popular mouse cell isolation workflows.
Figure 2. High-Purity Mouse B Cell Isolation Using EasySep™
Starting with mouse splenocytes, the B cell content (CD19+CD3-) of the isolated fraction is 97.6 - 99.3% using the EasySep™ Mouse B Cell Isolation Kit (Catalog #19854) and EasySep™ Magnet (Catalog #18000).
Figure 3. High-Purity Mouse CD4+ T Cell Isolation Using EasySep™
Starting with mouse splenocytes, the CD4+ T cell content (CD3+CD4+) of the isolated fraction ranges from 95.4 - 98.4% using the EasySep™ Mouse CD4+ T Cell Isolation Kit (Catalog #19852) and EasySep™ Magnet (Catalog #18000).
I currently use the EasySep™ Mouse T Cell Isolation Kit, CD4+ T Cell Isolation Kit, and CD8+ T Cell Isolation Kit. I have used different isolation kits over the years and these yield superior results, in my opinion.
I have also used Biovision, Thermofisher, Novus, and Miltenyi for T cell and monocyte isolation. I got better purity and viability with STEMCELL kits in comparison, and the isolation protocols for the STEMCELL kits are also less time consuming.
Cori Fain, PhD Student, Mayo Clinic
Streamline your mouse T cell research, from cell isolation with EasySep™ to culture, activation, expansion, and differentiation with ImmunoCult™. Explore EasySep™ mouse T cell isolation kits for CD4+, CD8+, naïve, memory, regulatory, and other specialized T cell subsets.
Figure 4. EasySep™ Isolation of Mouse CD11b+ Cells Achieves Comparable or Higher Purity and Recovery than Column-Based Methods
CD11b+ cells were isolated from mouse spleen by positive selection using EasySep™ Mouse CD11b Positive Selection Kit II (Catalog #18970) or a column-based alternative. Both the competitor's standard protocol and their optional "high purity" protocol, which requires an additional column, were tested. EasySep™ cell isolation yielded comparable or better (A) purity and (B) recovery. Data shown as mean ± SEM; n = 4 - 6.
Struggling to calculate cell recovery or measure purity after cell isolation? This quick guide walks you through both, including cell counting and flow cytometry tips to help you get reliable results.
Use Table 1 below to find the right EasySep™ mouse cell isolation kit for your cell type and tissue source, and compare typical cell purities and protocol durations across common cell types, including T cells, NK cells, and dendritic cells from splenocytes, as well as monocytes from peripheral blood (PBMCs), and more.
Table 1. Typical Cell Purity and Isolation Times for Common Mouse Cell Types Using EasySep™
| Mouse Cell Type (EasySep™ Kit) | Tissue/Sample Source | Typical Cell Purity (%) | Estimated Protocol Duration (Minutes)* |
|---|---|---|---|
| B Cells | Spleen | 96 - 99 | 15 |
| Pan-B Cells (including B-1, B-2 & Plasma Cells) | Spleen | 91 - 98 | 10 |
| T Cells | Spleen | 95 - 99 | 15 |
| CD4+ T Cells | Spleen | 92 - 98 | 15 |
| CD8+ T Cells | Spleen | 94 - 95 | 17.5 |
| Regulatory T Cells (Tregs; CD4⁺CD25⁺) | Spleen | 70 - 93 | 72.5 |
| Regulatory T Cells (Tregs; CD4⁺CD304⁺) | Spleen | 88 - 94 | 41.5 |
| Lymph Nodes | 91 - 93 | 41.5 | |
| Pan-Naïve T Cells | Spleen | 90 - 97 | 15 |
| NK Cells | Spleen | 67 - 89 | 25 |
| Dendritic Cells | Spleen | 52 - 63 | 13 |
| Monocytes | Bone Marrow | 85 - 94 | 19 |
| Macrophages (F4/80+ Cells) | Spleen | 87 - 93 | 27 |
| Lung | 92 - 95 | 35 | |
| Peritoneal Lavage | 97 | 24 | |
| Liver | 80 - 90 | 30 | |
| Myeloid-Derived Suppressor Cells (MDSCs; CD11b⁺Gr1⁺) | Naïve C57BL/6 Splenocytes | 81 - 91 | 18 |
| Tumor-Bearing BALB/c Splenocytes | 92 - 96 | 18 | |
| Hematopoietic Progenitor Cells | Bone Marrow | 60 - 84 | 31 |
*Protocol duration is based on the incubation, separation, and centrifugation steps described in the Product Information Sheet (PIS) and does not account for sample preparation, handling, or user-dependent processing time.
Note: Additional kits for specialized cell populations and subtypes are available. The cell purity values shown above are kit-specific data from the “Data” section of each Product Information Sheet (PIS).
Mouse Immune Cell Types, Frequencies & Markers
Reference cell frequencies, percentages of total leukocytes, phenotypic markers, and recommended EasySep™ kits for commonly studied mouse immune cell populations across spleen, bone marrow, peripheral blood, and more.
Integrated Workflow & Resources
Streamlined mouse cell isolation workflows begin with consistent sample preparation and generation of high-quality single-cell suspensions from mouse tissues using either manual or automated tissue dissociation methods. STEMprep™ supports automated tissue dissociation and generation of single-cell suspensions from mouse tissues. These suspensions can then be processed using EasySep™ to achieve simplified isolation of target cell populations for applications such as immune profiling, flow cytometry, and translational research. Explore the resources below for mouse sample preparation tools, cell isolation protocols, and downstream applications.
Step 1: Mouse Sample Preparation
Discover video and written protocols featuring tissue-specific workflows optimized for downstream cell isolation with EasySep™ mouse cell isolation kits.
Supported tissues include:
- Spleen (B, T, NK cells, etc.)
- Bone marrow (hematopoietic progenitors, monocytes, etc.)
- Brain (CD11b+ cells)
- Lung (ILC2 enrichment)
- Solid tumors (CD45+ tumor-infiltrating leukocytes)
- Liver (F4/80+ cells), and more.
Manual Tissue Processing & Single-Cell Suspension Protocols
How to Prepare a Single-Cell Suspension from Primary Tissue Samples Through Mechanical Digestion (e.g. Mouse Spleen)
How to Prepare a Single-Cell Suspension from Mouse Spleen Prior to Dendritic Cell Isolation
How to Prepare a Single-Cell Suspension from Mouse Brain Tissue
How to Prepare a Single-Cell Suspension from Mouse Lung Tissue
How to Prepare a Single-Cell Suspension from Mouse Solid Tumor
Preparation of Tissue Samples for Cell Separation
How to Isolate Mouse Bone Marrow Cells by Centrifugation
How to Manually Dissociate Mouse Liver Tissue into a Single-Cell Suspension
How to Isolate Mouse Peritoneal Cells
Automated Tissue Dissociation with STEMprep™
Automate and standardize tissue dissociation with the STEMprep™ Tissue Dissociator, a modular system designed to generate high-yield, high-viability single-cell suspensions while preserving epitope integrity and cell functionality.
Elevate Tissue Dissociation with STEMprep™
Request a demo today to see STEMprep™ in action and discover a more efficient way to optimize your tissue processing workflow.
Step 2: Simplified Mouse Cell Isolation with EasySep™
Explore EasySep™ mouse cell isolation resources, get free access to our On-Demand Mouse Immune Cell Isolation Course, discover featured CD45+ cell isolation workflows, and request a free sample to test EasySep™ yourself:
Try EasySep™ Magnetic Cell Separation
Curious about how EasySep™ can simplify your mouse cell isolation workflow? Explore our EasySep™ mouse cell isolation kits and request a free sample.
On-Demand Mouse Immune Cell Isolation Course
Register for our free, self-paced, virtual training course to learn how to process mouse tissue samples and easily isolate highly pure, functional immune cell types for your downstream applications using EasySep™ mouse kits.
Featured Mouse CD45+ Cell Isolation Workflows
Looking for specialized leukocyte isolation workflows? Explore the resources below for CD45+ cell enrichment from healthy tissues, tumors, and chimeric mice.
Mouse CD45+ Leukocyte Isolation from Healthy Tissues and Tumors
Compare CD45+ cell isolation workflows for healthy tissues and tumor samples based on tissue type, leukocyte frequency, and downstream applications.
Mouse CD45.1+ or CD45.2+ Cell Isolation for Chimerism and Adoptive Transfer Studies
Obtain highly pure, particle-free cells for chimerism analysis, adoptive transfer experiments, competitive transplantation studies, and downstream molecular applications.
Step 3: Downstream Applications for Mouse Cell Isolation
From immune profiling to molecular analysis, EasySep™-isolated mouse cells support the next step in your workflow. Explore the resources below to learn more about cell culture, molecular biology, and functional analysis.
Cell Culture
Explore workflows for cell expansion, maintenance, and cryopreservation.
Molecular Biology
Learn more about RNA and DNA isolation, genome editing, and transcriptomic analysis.
Cell Characterization and Functional Analysis
Discover tools for flow cytometry, cell counting, and immune profiling.
We received a kit for ILC2 enrichment from STEMCELL. We used the enrichment kit before sorting ILC2s, which allowed us to obtain more ILC2s from fewer mice in a shorter time period. Due to this increased sorting efficiency, we were able to perform a transplant experiment, which was one of the key revision experiments that led us to our recently published paper in Immunity.
Fumio Takei, PhD, Distinguished Scientist, Terry Fox Laboratory and Professor, The University of British Columbia
If you have any questions, contact us at techsupport@stemcell.com.
