Single-Cell Multiome (scRNA + scATAC)
What Is Single-Cell Multiome (scRNA + scATAC)?
Single-Cell Multiome sequencing is a dual-modality NGS technique that simultaneously profiles both gene expression and chromatin accessibility within the same single cell. By combining scRNA-seq and scATAC-seq, this method offers an unprecedented view of gene regulatory dynamics—revealing how changes in chromatin structure influence transcriptional outcomes at the individual cell level.
This powerful approach bridges transcriptomics and epigenomics in a single workflow, providing deeper insight into cell state, identity, and function than either assay alone. It is particularly valuable in complex tissues or disease states where regulation is tightly controlled and heterogeneous.
At AUGenomics, we leverage multiomic platforms (including workflows compatible with Parse Biosciences, Scale Biosciences, and CS Genetics) to capture both regulatory and transcriptional landscapes in a single experiment. This integration allows researchers to link open chromatin regions to active gene expression, revealing cause-and-effect relationships that bulk or single-modality assays cannot uncover.
Advantages of Single-Cell Multiome (scRNA + scATAC)
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Dual Modality Data: Captures chromatin accessibility and RNA expression from the same cell.
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Regulatory–Transcriptional Linkage: Directly associates open regulatory elements with gene expression changes.
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High-Resolution Cellular Insights: Identifies how epigenetic states control cell identity and function.
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Rare Population Characterization: Uncovers epigenetic and transcriptional features of low-frequency cell types.
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Multi-Platform Expertise: Supports leading multiome-compatible workflows, ensuring flexibility for diverse samples.
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Broad Sample Support: Compatible with fresh and cryopreserved nuclei from a wide range of tissues.
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Advanced Bioinformatics: Integrates scRNA and scATAC data into unified cell state maps, peak-to-gene linkages, and transcription factor motif analyses.
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Customizable Workflows: Tailored sequencing depth, analysis scope, and reporting to fit research goals.
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Multi-Omic Integration: Data can be combined with immune receptor profiling, methylation, or proteomics for even richer datasets.
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Expert Guidance: From sample handling through multiomic interpretation, we collaborate with you every step of the way.
Single-cell multiome sequencing provides functional and regulatory context that drives new discoveries in immunology, oncology, neuroscience, and beyond. Applications include:
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Cell Fate Mapping: Linking chromatin changes to transcriptional programs during differentiation.
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Cancer Research: Profiling tumor heterogeneity with both gene expression and epigenetic regulation layers.
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Immunology: Understanding activation, exhaustion, and epigenetic control of immune cell subsets.
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Developmental Biology: Tracing lineage specification and identifying regulatory drivers of organogenesis.
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Disease Mechanism Studies: Detecting epigenetic dysregulation that leads to altered transcriptional states.
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Drug Response Assessment: Monitoring how therapies remodel chromatin accessibility and downstream expression.
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Transcription Factor Network Analysis: Identifying regulatory elements controlling cell-type–specific programs.
What is Single-Cell Multiome (scRNA + scATAC) Used For?
Single-Cell Multiome (scRNA + scATAC) with AUGenomics
Sample Submission
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Sample types accepted: Fresh or cryopreserved single-cell suspensions from tissues, tumors, or organoids
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Recommended input: Minimum 20,000–50,000 cells per sample to ensure robust cell capture and dual profiling
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Sequencing specifications:
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Paired-end reads for both modalities
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20,000–50,000 reads per cell for RNA; 25,000–50,000 reads per cell for ATAC
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≥5,000 cells/sample post-QC suggested
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Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
4–6 weeks from sample QC to data delivery.
Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: How is data from both modalities linked in multiome sequencing?
A: Since both assays are performed on the same single cell, the resulting scRNA and scATAC data are barcoded and aligned, enabling direct comparison and integrative analysis.
Q: How does single-cell multiome differ from running scRNA-seq and scATAC-seq separately?
A: Running the assays separately captures unlinked datasets from different cells. Multiome sequencing measures both modalities in the same cell, enabling direct peak-to-gene linkage and regulatory network inference.
Q: How many cells can be analyzed?
A: Depending on the platform, we can process thousands to tens of thousands of nuclei per experiment.
Q: Can this data be integrated with other omics layers?
A: Yes. Multiome data pairs naturally with methylation, proteomics, or immune receptor profiling for a comprehensive systems biology approach.
Q: How do I preserve cells for scRNA-seq or multiome if I can’t process them immediately?
A: Stabilization buffers or cell fixation may be options, depending on the platform. Contact us for guidance on your specific sample type.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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Multiome: Refers to the integration of two or more molecular readouts from the same single cell
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Gene Expression: The process by which information from a gene is transcribed into RNA
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Chromatin Accessibility: The availability of DNA regions for regulatory binding
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Enhancer–Gene Linkage: The process of connecting distal regulatory elements with their target genes
