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PSC Characterization Tools
Verifying the identity, quality, and genomic stability of pluripotent stem cells (PSCs) is essential for reliable downstream applications. Our portfolio of cellular and molecular characterization tools enables fast, accurate, and cost-effective validation of PSC lines—from pluripotency confirmation to genomic integrity assessment.
From gene expression profiling assays to pluripotency marker antibodies and genomic stability arrays, these solutions support every stage of PSC characterization.
Overview of PSC characterization methods
Use complementary approaches to confidently assess pluripotency and cell line quality:
- Marker-based detection (immunostaining)—Identify pluripotency-associated surface and intracellular markers
- Gene expression assays—Evaluate pluripotency and differentiation potential (e.g., TaqMan hPSC Scorecard Panel)
- Functional differentiation assays—Confirm trilineage differentiation potential
- Genomic stability analysis—Detect chromosomal abnormalities (e.g., KaryoStat Assays)
Compare PSC characterization methods
| Alkaline Phosphatase Live Stain | Antibody staining | TaqMan hPSC Scorecard Panel | KaryoStat and KaryoStat HD Assays | |
|---|---|---|---|---|
| Key benefit | Easy identification of pluripotency without compromising cell integrity | Specific and flexible identification of PSCs | Evaluates pluripotency and confirms trilineage differentiation potential | Alternative to g-banding karyotyping; offers whole-genome coverage for accurate detection of chromosomal abnormalities |
| Specificity | Low (stains stem and progenitor cells) | Medium (stains human ES and iPS cells) | High (profiles expression of both PSC markers and early germ layer factors) | High |
| Cell viability | Yes | No [1] | No | No |
| Time to results | ~20 min | 90–120 min | 6–8 hours | 3–4 days |
| Are data analysis tools included? | No | No | Yes, free cloud-based software | Yes, free downloadable Chromosome Analysis Suite (ChAS) software |
| Is a reference standard included? | No | No | Yes [2] | No |
| Are EVOS imaging system protocols available? | Yes | Yes | N/A | No |
| Training and expertise required | Minimal | Minimal | Moderate | Moderate |
| Unit size | 500 μL vial sufficient for staining twelve 6 cm dishes | 100 μg | 1,384-well plate kit (4 samples/plate) or 2 × 96-well plates (1 sample/plate) | 24 arrays (one sample/array) |
| Order | Order | Order | Learn more | |
2. Reference standard is included in free software. | ||||
How to choose the right pluripotency detection method
Selecting the appropriate method depends on your workflow stage and required confidence level:
- Use surface markers for rapid screening and live-cell analysis
- Use transcription factor markers (e.g., OCT4, NANOG) for deeper pluripotency confirmation
- Combine multiple markers to increase confidence and reduce false positives
- Match the method to your workflow stage:
- Early screening → live stains or surface markers
- Verification → gene expression assays + intracellular markers
Pluripotent stem cell antibodies and detection kits
Verifying cell line quality is critical to stem cell research. Therefore, we offer you maximum flexibility in antibody and dye choices to enable you to specifically detect your pluripotent stem cells (PSCs) and their derivatives.
Immunocytochemistry and live-cell imaging kits
Key reagents you need for superior image-based analysis of hPSCs and a variety of lineages are now available in one box. Introducing Molecular Probes Immunocytochemistry and live imaging kits for stem cells. Kits offer a combination of antibodies, stains, buffers, and/or media to create beautiful, high-quality images of stem cells.
Pluripotent state detection kits
Immunocytochemistry kits
Live cell staining kits
Differentiated state detection kits
Immunocytochemistry kits
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Figure 1. Analysis of OCT4 and SSEA4 expression in iPSCs using the PSC 4-Marker ICC Kit. Induced pluripotent stem cells (iPSCs) derived from CD34+ cord blood (Gibco Human Episomal iPSC Line) were grown under feeder-free conditions using Essential 8 Medium in wells coated with vitronectin. The cells were stained for pluripotency markers using the PSC 4-Marker ICC Kit.
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Figure 2. Surface marker analysis of feeder-dependent PSC cultures using dye-conjugated antibodies for TRA-1-60 (red) as a positive marker and CD44 (green) as a negative marker for pluripotency.
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Figure 3. iPSCs were differentiated for 14 days using the PSC Cardiomyocyte Differentiation Kit. The cells were stained using the Human Cardiomyocyte Immunocytochemistry Kit for the following markers: NKX2.5 (red) for early cardiac mesoderm and TNNT2/cTNT (green) for cardiomyocytes along with DAPI nuclear DNA counterstaining (blue).
Which markers are used to identify pluripotent stem cells?
Common pluripotency markers include:
- OCT4 (POU5F1): Core transcription factor for maintaining pluripotency
- NANOG: Self-renewal and pluripotency regulator
- SSEA-3/SSEA-4: Surface glycolipid antigens
- TRA-1-60/TRA-1-81: Surface markers for undifferentiated PSCs
- E-Cadherin: Cell adhesion marker associated with pluripotent state
What is the difference between surface and intracellular pluripotency markers?
Surface markers (e.g., SSEA-4, TRA-1-60)
- Enable live-cell staining and sorting
- Well-suited for non-destructive monitoring
Intracellular markers (e.g., OCT4, NANOG)
- Require cell fixation and permeabilization
- Enable deeper confirmation of pluripotent state
| Target Antigen | Reactivity | Host | Clonality | Validation | Cat. No. |
|---|---|---|---|---|---|
| E-Cadherin | Human | Mouse | Monoclonal | WB, IHC, IP, IF, FC, ELISA | 13-1700 |
| TRA 1-60 | Human | Mouse | Monoclonal | WB, IHC, IF, FC, ELISA | 41-1000 |
| TRA 1-81 | Human | Mouse | Monoclonal | WB, IHC, IF, FC, ELISA | 41-1100 |
| SSEA-3/4 | Human, Mouse | Mouse | Monoclonal | IHC, IF, FC | 41-4000 |
WB = Western Blot; IHC = Immunohistochemistry; IP = Immunoprecipitation; IF = Immunofluorescence; FC = Flow Cytometry
These primary antibodies can be conjugated directly with Alexa Fluor Dyes or combined with our vast suite of secondary conjugated antibodies. Stained cells can be visualized with EVOS Imaging Systems (Figures 4-6).
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Figure 4. H9 hESCs were grown on feeders and stained (without fixing) with SSEA-4 primary antibody and an Alexa Fluor 488–conjugated anti–mouse IgG secondary antibody. The cells were visualized at 100x magnification using a FITC filter.
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Figure 5. H9 hESCs were grown on feeders and stained (without fixing) with TRA-1-81 primary antibody and an Alexa Fluor 488–conjugated anti–mouse IgG secondary antibody. The cells were visualized at 50x magnification. Shown is a merged image using phase contrast and a FITC filter.
Click image to enlarge
Figure 6. H9 hESCs were grown on feeders, fixed with PFA, stained with TRA-1-60 primary antibody and an Alexa Fluor 488–conjugated anti–mouse IgG secondary antibody, and counterstained with DAPI nuclear stain. The cells were visualized at 50x magnification. Shown is a merged image using phase contrast, and FITC and Hoescht filters.
Key considerations when using pluripotent stem cell antibodies
- Use multiple markers to help ensure robust confirmation of pluripotency
- Optimize timing of staining after reprogramming or passaging
- Minimize false positives from partially differentiated cells
- Help maintain consistency across experiments and operators
KaryoStat assays for assessing genomic stability of PSC lines
Genomic stability is a critical quality attribute for pluripotent stem cells. The KaryoStat and KaryoStat HD Assays offer a high-resolution alternative to traditional karyotyping, enabling genome-wide detection of chromosomal abnormalities.
Why use KaryoStat Assays for iPSC genomic stability analysis
- The assay includes arrays, reagents, and easy-to-use data analysis software for a cost-effective and streamlined analysis of pluripotent stem cell lines
- Genome-wide detection of copy number variations (CNVs)
- Faster turnaround time with results in 3 to 4 days
- Simultaneous karyotyping and genotyping (sample ID) with one assay
- Designed specifically for pluripotent stem cell workflows
- Simple analysis tool that does not require cytogenetics expertise
Instrument requirements
KaryoStat and KaryoStat HD Arrays are compatible with GeneChip Scanner 3000.
KaryoStat data analysis
The KaryoStat and KaryoStat HD Assays include access to free downloadable Chromosomal Analysis Suite (ChAS) Software that allows researchers to confirm absence of chromosomal abnormalities in PSC lines.
What is the difference between KaryoStat and KaryoStat HD Assay?
KaryoStat Assay has a resolution similar to g-banding karyotyping and is recommended for most stem cell research applications. The KaryoStat HD Assay provides higher resolution analysis with greater than 99% sensitivity and can reliably detect 25–50 kb copy number changes across the genome at high specificity with single-nucleotide polymorphism (SNP) allelic corroboration.
| KaryoStat Assay | KaryoStat HD Assay | |
|---|---|---|
| Gains | >2 Mb | >25–50 kb |
| Losses | >1 Mb | >25–50 kb |
| Absence of heterozygosity | >5 Mb | >1 Mb |
| SNP | Yes | Yes |
| Coverage | Low | Highest |
Ordering information
KaryoStat Assays include arrays and reagents for 24 reactions and access to free data analysis software.
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Intended use of the products mentioned on this page vary. For specific intended use statements please refer to the product label.
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