Single-cell RNA sequencing (scRNA-seq) technologies have advanced quickly in recent years. One of the most impactful developments is the ability to work with fixed samples. This innovation allows researchers to collect, preserve, and ship material with fewer constraints, opening new possibilities in both basic research and clinical studies.
Currently, at Single Cell Discoveries (SCD), we support three major workflows compatible with fixed samples:
- Flex Gene Expression (Flex), from 10x Genomics
- QuantumScale Single Cell RNA (QuantumScale) from Scale Biosciences, now part of 10x Genomics
- Evercode WT from Parse Biosciences
In this article, we outline the key features of each solution and help you determine which option best fits your research goals.
Why Fixed Samples Matter
- Flexibility: Samples can be fixed and stored until processing. This is valuable for fieldwork, delayed deliveries, or time-course experiments that require batching
- Safety: Fixation inactivates pathogens, making infectious or hazardous samples safer to handle.
- Data quality: Fixation reduces variability during sample handling and can improve reproducibility.
- Preservation: Fixation pauses cellular processes, capturing the biological state at the moment of collection. This also reduces degradation and is particularly useful for fragile tissues, biopsies, or xenograft models.
- Collaboration: Fixation allows multicenter projects and clinical trials to centralize processing at a single laboratory. For example, you can fix your samples at your lab and send them directly to SCD for processing.
For these reasons, fixed-sample workflows have become central to many scRNA-seq projects. At SCD, we offer a full range of options to ensure every study gets the flexibility it needs.
Get the 10x Genomics
information guide
You can find a full explanation of 10x Genomics, its variations, and our approach in our information guide.
Flex Gene Expression (Flex)
Technology
Flex builds on the widely adopted 10x Genomics droplet-based platform, Chromium X, but uses probe-based chemistry designed specifically for fixed material. The probe panels target protein-coding genes, providing near whole transcriptome coverage.
In singleplex mode, a Flex run can process eight samples in parallel, with each sample yielding up to ~20,000 cells or nuclei. When multiplexing, however, Flex can process up to 320k cells per lane and 2.5 million on a full chip.
Sample compatibility
Flex accepts different inputs: solid or liquid biological tissues, cells, nuclei in suspension, and organoids. It works with fresh, frozen, and formalin-fixed samples, including formalin-fixed paraffin-embedded tissues (FFPE).
Standard probe sets are available for human and mouse, and custom panels can be designed for other species or specific targets.
Additional Features
- Sample multiplexing: Probe barcodes can be used to uniquely label samples before pooling. Currently, up to 16 samples can be combined in a single channel and later computationally separated. This increases throughput and reduces batch effects.
- Protein profiling: Flex is compatible with 10x’s antibody-based Feature Barcoding technology, including TotalSeq™-B and -C antibodies and the MultiPro™ Fixed Cell Immune Profiling Antibody Cocktail. These tools enable both cell surface protein profiling (CITE-seq) and intracellular protein detection.
- CRISPR guide capture: Custom probes can capture CRISPR guide RNAs at the single-cell level, enabling pooled CRISPR knockout or activation screens.
- Specific genes: Custom probe sets can be designed to target specific transcripts—for example, GFP or a virus.
When to Choose Flex
- Working with FFPE samples.
- Studies focused on protein-coding genes.
- Projects requiring protein-coding mRNA and specific transcript(s) detection.
- Projects that may later expand and use the same probe set for spatial transcriptomics with 10x Genomics technology.
- When multiomics experiments require intracellular protein detection.
Study an example Exploratory Data Report
After each sequencing project, you will receive a data report with a comprehensive and easily accessible exploration of your data. Have a look at an example of our 10x Genomics Flex FFPE data report.
QuantumScale Single Cell RNA (QuantumScale)
Technology
QuantumScale from Scale Biosciences, now part of 10x Genomics, relies on Quantum Barcoding, a new split-pool barcoding strategy that relies on microwells and oligo-coded barcode beads. Cells or nuclei are labeled through three successive barcoding steps, enabling scalability from tens of thousands to millions of cells. It requires a specific plate, the quantum barcoding plate, plus standard lab equipment. This is a whole transcriptome method.
The kit is available in multiple formats to match project size:
- Medium Kit: up to ~168,000 cells per run
- Large Kit: up to ~2 million cells per run
- Extra-Large (XL) Kit: up to ~4 million cells per run
Sample compatibility
QuantumScale works with fresh, frozen, and fixed material (ideally, prepared with the Scale Biosciences recommended protocol). It supports cells or nuclei in suspension isolated from cell cultures, biological tissues, or organoids. The chemistry is species-agnostic, targeting poly(A)+ RNA from any organism. Read more about single-cell sequencing non-model species here.
Additional Features
- Sample multiplexing (ScalePlex): Special probe barcodes can be used to uniquely label samples before fixation and pooling. Up to 9216 samples can be combined in the biggest format of the kit and later computationally separated. This increases throughput and reduces batch effects. It is also an economical advantage.
When to Choose QuantumScale
- Projects requiring very high throughput (up to ~4 million cells/run).
- Studies that are expected to scale from smaller pilot runs to larger datasets without changing technology.
- Experiments that need whole-transcriptome coverage.
- Large-scale studies with tight timelines.
Evercode WT from Parse Biosciences
Technology
Evercode Whole Transcriptome (WT) kits, from Parse Biosciences, use split-pool combinatorial barcoding, labeling cells or nuclei through successive steps in 96-well plates, combined with commonly available laboratory equipment. This enables whole-transcriptome profiling from thousands up to millions of cells in a single experiment.
Available formats include:
- Evercode WT Mini: up to ~10 thousand cells per run
- Evercode WT: up to ~100 thousand cells per run
- Evercode WT Mega: up to ~1 million cells per run
- Evercode WT Penta: up to ~5 million cells per run
Sample Compatibility
Evercode WT supports fresh, frozen, and fixed samples (ideally, prepared with Parse Biosciences’ recommended protocol). Works with cells or nuclei in suspension isolated from cell cultures, liquid and solid tissues, or organoids. It is also species-agnostic for poly(A)+ RNA.
Additional Features
- TCR profiling: Captures paired TCR α/β chains with whole transcriptomes.
- BCR profiling: Captures paired immunoglobulin heavy and light chains with whole transcriptomes.
- CRISPR guide detection: Identification of CRISPR guide RNAs at the single-cell level.
- Selected Genes: Targeted sequencing options, either pre-designed (Immune1000) or custom.
When to Choose Evercode WT
- Projects requiring very high throughput (up to ~5 million cells/run).
- Studies that are expected to scale from smaller pilot runs to larger datasets without changing technology.
- Large projects requiring immune repertoire profiling (TCR/BCR).
- High-throughput functional genomics screens with CRISPR perturbations.
- Projects requiring whole transcriptome and specific transcript(s) detection
How to Choose the Right Workflow for Your Project
If your project already uses technology from one of the mentioned companies, if possible, it is better to continue with it. This will make data integration more straightforward and help avoid potential batch effects or bias.
For new projects, the right choice depends on your research goals. The figure below summarizes the main characteristics of each kit and highlights the scenarios where each is the best fit.
Fig. 1. Key Differences Between Flex, QuantumScale and Evercode WT. Comparison of the three main scRNA-seq workflows for fixed samples currently offered by SCD, highlighting their technology, sample compatibility, transcriptome coverage, scalability, and unique features.
Conclusion
At SCD, we support all the previous scRNA-seq workflows. Our team guides researchers through project design, platform selection, and data delivery. Whether you need FFPE compatibility, high-throughput discovery, immune repertoire analysis, or CRISPR screen integration, we help you identify the workflow that maximizes value for your research.
Contact us to discuss your project and determine which fixed-sample solution is the right fit.
