iPSC Characterization Services

Why iPSC Characterization Matters

iPSCs are inherently sensitive, highly plastic, and prone to genomic or phenotypic drift during culture. Without systematic characterization, even subtle abnormalities can compromise the reproducibility of differentiation, distort disease phenotypes, or generate misleading conclusions. Robust evaluation therefore becomes essential for safeguarding both the scientific integrity of your project and the translational potential of your iPSC lines.

High-quality characterization matters for several critical reasons:

Confirming True Pluripotency: Marker expression (OCT4, SOX2, NANOG), teratoma assays, EB formation, and qPCR validation ensure that the cells retain the molecular signatures necessary for consistent performance across studies.
Ensuring Genomic Stability for Downstream Reliability: Karyotype analysis ensures researchers work with genetically stable lines suitable for disease modeling, drug screening, and translational research.
Supporting Functional Competence: Beyond molecular markers, functional readouts—such as electrophysiological activity from MEA assays—demonstrate whether differentiated cells perform as expected. For applications involving neurons or cardiomyocytes, functional validation is indispensable for assessing maturity, excitability, and responsiveness to compounds.

Our iPSC Characterization Services

Services	Descriptions
Morphology of iPSC	Cell morphology provides the earliest visual indicator of stemness and culture quality. Our specialists assess: Colony borders and compactness Nucleus-to-cytoplasm ratio Nucleoli prominence Presence of differentiated cell types Colony uniformity and confluency High-resolution imaging reports are delivered along with expert interpretation.
Teratoma Formation Assays for iPSC	Teratoma assays represent the gold standard for pluripotency evaluation in vivo. We offer: Immunodeficient mouse implantation In vivo differentiation into ectoderm, mesoderm, and endoderm Histopathological analysis H&E staining with high-resolution image documentation This assay confirms authentic tri-lineage potential before clinical-scale research.
Embryoid Body (EB) Formation and Characterization for iPSC	EB formation replicates spontaneous differentiation in a controlled, 3D culture environment. Our workflow includes: Suspension-based EB induction Time-course monitoring Gene expression analysis for tri-lineage markers Morphological scoring Optional directed differentiation follow-up assays EB data provides strong evidence of developmental competence.
Karyotype Analysis for iPSC	Genomic stability is essential for safety, differentiation reliability, reproducibility, and regulatory acceptance. We provide: G-banding karyotyping Chromosomal aberration screening Identification of structural and numerical abnormalities Integrated reporting with risk interpretation Clients use our karyotype data to ensure high-quality downstream differentiation.
Gender Determination of iPSC	Sex chromosome identity may influence differentiation efficiency and disease-model relevance. Creative Biolabs offers: PCR-based gender identification Chromosome-based confirmation Data supporting XX/XY lineage verification This service is crucial for personalized medicine, iPSC banking, and lineage-specific studies.
Electrophysiological Characterization via Multi-electrode Array (MEA) for iPSC	MEA analysis provides functional readouts particularly important for iPSC-derived neurons and cardiomyocytes. Our capabilities include: Spontaneous action potential recording Network activity quantification Field potential assessments Drug response profiling High-throughput MEA platforms These assays confirm that iPSC-derived cells display appropriate electrophysiological phenotypes.
qPCR Analysis for Pluripotency Markers for iPSC	Gene expression analysis ensures that your iPSC lines maintain high pluripotency. We evaluate key markers such as: OCT4 SOX2 NANOG KLF4 LIN28 Reports include Ct values, stability analysis, relative expression, and assay performance metrics.
Pluripotency Marker Assays for iPSC	Using immunofluorescence and flow cytometry, we evaluate surface and intracellular markers including: SSEA-3 / SSEA-4 TRA-1-60 / TRA-1-81 OCT4, SOX2, NANOG protein expression These assays confirm stemness at the phenotypic and protein levels, supporting both QC and publication needs.

Get Started Today!

Technology Platforms Supporting Our Characterization Assays

We leverage a broad suite of high-precision instruments:

High-content imaging systems for morphology and immunostaining
qPCR and digital PCR platforms
Flow cytometry systems
G-banding cytogenetics platforms
MEA electrophysiology arrays (high-throughput)
Automated histology systems
Spectral imaging platforms for marker quantification
Genomic QC systems (optional add-on: CNV detection, STR profiling)

This robust infrastructure ensures high data fidelity and rapid delivery.

Discuss Your Project!

How We Solve The Key Challenges in iPSC Characterization

Characterizing iPSCs is technically demanding due to their plasticity and sensitivity. Creative Biolabs helps clients overcome typical bottlenecks.

Culture Variability Between Laboratories - Even minor differences in media, feeder systems, or passaging protocols may alter pluripotency.
Our solution: standardized SOPs, harmonized culture conditions, and side-by-side comparisons with reference cell lines.
Genetic Instability During Extended Expansion - Long-term culture increases the risk of chromosomal abnormalities.
Our solution: periodic karyotyping and optional rapid genomic integrity screening.
Loss of Pluripotency - iPSCs may gradually lose stemness or partially differentiate.
Our solution: multi-parameter evaluation including morphology, immunostaining, qPCR, and EB assays to detect early deviations.
Inefficient or Inconsistent Differentiation - Inadequate initial quality leads directly to poor differentiation performance.
Our solution: teratoma and EB formation assays that confirm tri-lineage potential prior to downstream applications.
Lack of Functional Validation - Some projects require proof that differentiated cells behave as expected.
Our solution: high-resolution MEA electrophysiology for neurons/cardiomyocytes, paired with cell-type-specific markers.

Wide Applications of iPSC Characterization

High-quality iPSC characterization is not merely a quality-control requirement—it is the engine that drives the success of a broad spectrum of scientific, preclinical, and industrial programs. Robust characterization data ensures that the iPSC lines they rely on are genetically stable, phenotypically consistent, fully pluripotent, and capable of differentiating into functional, lineage-specific cells.

Below, we demonstrate how high-standard iPSC characterization can empower key application scenarios, according to industry needs and research processes.

Applications	Descriptions
Disease Modeling	Accurately representing patient-specific phenotypes (e.g., neurodegenerative, cardiovascular, metabolic disorders).
High-Throughput Drug Screening	Ensures differentiated cells respond reproducibly to candidate compounds.
Toxicity and Safety Evaluation	iPSC-derived hepatocytes, cardiomyocytes, and neurons form robust in vitro toxicity platforms.
Cell Therapy Development	Characterization ensures genomic stability, lineage identity, and phenotype fidelity before moving to translational stages.
iPSC Banking & Reference Line Development	Standardized QC ensures long-term reliability of master and working cell banks.
Personalized Medicine	Sex verification and genomic stability are essential for individualized disease models.

Contact Us

Published Data

The researchers used the popular 3D floating culture method to generate retinal organoids from stem cells. This method starts with either small clumps of stem cells generated from larger clones (clumps protocol, CP) or with an aggregation of single cells (single cells protocol, SCP). Using histological analysis and gene-expression comparison, they found a retention of the pluripotency capacity on embryoid bodies generated through the SCP compared to the CP.

Fig. 1 Confocal imaging of EBs generated using the CP and the SCP at day 7.^1,3

The researchers discussed the different types of MEAs used for in vivo and in vitro recordings. They summarized 2D hPSC-derived neural cultures on MEA, their strengths, weaknesses, and what kind of information they can provide us on the physiology and pathology of neuronal networks. As organoids and other hPSC-derived 3D models have already been in use for several years, they took a similar look into their MEA data, their ins, outs, and how they can describe the structure and function of the human brain.

Functional characterization of hPSC-derived models with MEA. (OA Literature)

Fig. 2 MEA recordings of the human brain and corresponding hPSC-derived models.^2,3

What Our Clients Say

"We sent Creative Biolabs several newly reprogrammed iPSC lines. Their morphology assessment, pluripotency staining, and qPCR analysis were extremely thorough. The report not only confirmed pluripotency but also highlighted early differentiation tendencies we hadn't noticed. This level of detail saved us months of downstream troubleshooting."

— Principal Investigator, Stem Cell Biology Lab

"Our team needed stable and well-characterized iPSC lines for a neurological screening platform. Creative Biolabs provided prompt karyotype results, clear EB differentiation data, and a clean QC package that our automation team could rely on. It made our transition to screening much smoother."

— Director of Drug Discovery, Mid-size Biopharma

"We worked with their MEA team to validate our iPSC-derived neurons. The field potential recordings, spike analysis, and network activity metrics were highly detailed. Their scientific support helped us interpret the patterns and prepare figures for a manuscript."

— Senior Scientist, Neuroscience Program

"Some of our disease models are sex-specific. Creative Biolabs helped us validate XX/XY identity and confirm the authenticity of each iPSC line. Their responsiveness and scientific clarity make them easy to work with."

— Group Leader, Personalized Medicine Research Center

FAQs

Q: What level of characterization is recommended before starting an iPSC differentiation project?

A: A comprehensive panel including morphology assessment, pluripotency marker profiling, qPCR validation, and karyotype analysis is typically sufficient. For projects involving functional cell types such as neurons or cardiomyocytes, EB formation assays and optional MEA evaluations are strongly recommended.

Q: Can Creative Biolabs work with iPSC lines generated from Sendai, episomal, mRNA, or viral reprogramming?

A: Yes. Our team routinely characterizes iPSC lines produced through all common reprogramming strategies. We also evaluate transgene silencing when required, ensuring your lines reach a stable, integration-free state suitable for downstream studies.

Q: How many cells should we prepare for a full characterization package?

A: For most assays, 1–2 × 10⁶ cells per module are sufficient. Teratoma, MEA, and multi-step marker assays may require additional starting material. We provide a detailed submission guideline to ensure you can allocate samples efficiently and avoid unnecessary repeats.

Q: Can results from multiple characterization assays be combined into a single integrated report?

A: Absolutely. Most clients prefer an integrated report for easier regulatory submission, publication preparation, and internal review. We compile raw data, analysis summaries, microscopy images, electrophysiology outputs, and QC interpretation into one structured package.

Q: What if our iPSC line has minor chromosomal abnormalities? Can we still proceed?

A: This depends on the application. Some aberrations may not influence basic research but are unacceptable for preclinical, translational, or therapy-focused projects. Our team provides interpretation and risk assessment to help you decide next steps or select alternative clones.

Q: What quality controls are performed before you begin characterization?

A: Every sample undergoes initial viability assessment, morphological inspection, and contamination screening, including optional mycoplasma testing. These checks ensure that assays reflect intrinsic cell quality rather than external culture issues.

Get Started with Confidence

1. Contact Us

via the Inquiry Form or Email

2. Define Your Needs

Cell Type, Function, Quantity, Modifications

3. Kickstart the Project

Our Expert Team Guiding Every Step

High-quality data is the foundation of reliable stem cell research. Creative Biolabs combines industry-leading technology platforms with deep scientific expertise to deliver comprehensive, reproducible, and actionable iPSC characterization.

Contact us today to discuss your project or request a customized quote.

References

Heredero Berzal, Andrea, et al. "The Analysis of Embryoid Body Formation and Its Role in Retinal Organoid Development." International Journal of Molecular Sciences 25.3 (2024): 1444. https://doi.org/10.3390/ijms25031444
Pelkonen, Anssi, et al. "Functional characterization of human pluripotent stem cell-derived models of the brain with microelectrode arrays." Cells 11.1 (2021): 106. https://doi.org/10.3390/cells11010106
Distributed under Open Access license CC BY 4.0, without modification.

Created November 2025