Single Cell Transcriptomics Comparison
Chromium Solutions
| Feature | Flex | Universal 3' Gene Expression (GEX) | Epi ATAC | Multiome (GEX+ATAC) | Immune profiling |
|---|---|---|---|---|---|
| Primary Insight | Transcriptome per cell | Transcriptome per cell | Chromatin accessibility | Integrated transcriptome + epigenome | Transcriptome + immune repertoire |
| Analytes Captured | mRNA (WT probe panel) | mRNA (oligo dT priming) | Open chromatin regions (DNA) | mRNA + chromatin accessibility | mRNA + TCR/BCR V(D)J regions |
| Cell Type Resolution | High | High | High | Very high | High + clonotype |
| Input Type | Cells, nuclei, fresh, fixed, FFPE tissue, fixed whole blood | Fresh or frozen single cells/nuclei | Nuclei (obtained from fresh/frozen tissue) | Nuclei | Fresh or frozen cells |
| Species Supported | Human, mouse | Human, mouse, other | Human, mouse, other | Human, mouse, other | Human, mouse |
| Throughput | 20,000 cells/sample | 20,000 cells/sample | 10,000 nuclei/sample | 10,000 nuclei/sample | 10,000 cells/sample |
| Data Type | Gene expression (probe-based counts) | Gene expression matrix | Peak/motif matrix | Joint gene + chromatin matrix | Gene + TCR/BCR sequence |
| Strengths | High-throughput FFPE, fixed samples, multiplexing | General cell atlas work | Regulatory landscape | Regulatory-expression linkage | T/B cell diversity, tumor-immune |
| Analysis Complexity | Moderate | Moderate | High (bioinformatics heavy) | Very high | High (multi-modal) |
| Sequencing Needs | Moderate | Moderate | High | Very high (dual library) | Higher (due to V(D)J enrichment) |
Choosing the Right Solution
- scRNAseq → Great for broad gene expression questions across many cell types.
- Epi ATAC → Use when studying epigenetic regulation, chromatin state or cell identity drivers.
- Multiome → Best for linking chromatin accessibility with gene expression in the same cell—ideal for deep regulatory insights.
- Immune Profiling → Essential for tracking T and B cell populations, especially in immunology or oncology.
When to Use Chromium Flex for scRNAseq
- Ideal for:
- Biobanked samples
- Multisite studies with pre-fixed cells
- High-throughput projects (20k+ cells)
- FFPE compatibility (with select workflows)
- Benefits:
- Workflow flexibility
- Easier logistics across collaborators
- Reduced batch effect potential
Need help determining which Chromium solution is right for your project? Reach out to the core for guidance on assay selection and sample prep.