Single-Cell Epigenome Profiling (scATAC-seq)
What Is Single-Cell Epigenome Profiling (scATAC-seq)?
Single-cell epigenome profiling is an advanced next-generation sequencing (NGS) method that maps chromatin accessibility, histone modifications, and other epigenomic features at the resolution of individual cells. Unlike bulk epigenomic assays that average signals across populations, this approach preserves cell-to-cell variability, uncovering regulatory differences that define cell identity, lineage, and disease states.
Using technologies such as single-cell ATAC-seq (scATAC-seq) and multiome assays (combined scATAC + scRNA-seq), AUGenomics enables researchers to:
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Interrogate chromatin landscapes at thousands of individual loci per cell.
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Resolve cell-type–specific regulatory signatures in complex tissues.
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Integrate chromatin state with gene expression, revealing how accessibility drives transcriptional programs.
This powerful technique generates multi-layered insights into how the epigenome orchestrates cellular behavior, developmental trajectories, and pathological remodeling. It is particularly valuable for research in oncology, immunology, neurobiology, and regenerative medicine where understanding regulatory heterogeneity is key.
Advantages of scATAC-seq
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High-Resolution Chromatin Mapping: Captures regulatory landscapes at single-cell resolution to identify cell-type–specific open chromatin regions.
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ultiome Capability: Integrates chromatin accessibility with RNA expression from the same cell for direct regulatory linkage.
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Regulatory Element Discovery: Identifies active enhancers, promoters, and transcription factor binding sites across heterogeneous samples.
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Flexible Sample Inputs: Compatible with both fresh and cryopreserved tissues or isolated nuclei.
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Low Input Requirements: Generates high-quality data from as few as 5,000 cells/nuclei.
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Customizable Workflows: Supports scATAC-seq, multiome, and other multi-modal epigenomic assays.
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Advanced Bioinformatics: Includes peak calling, motif analysis, trajectory inference, and peak-to-gene linkage.
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Cross-Species Support: Available for human, mouse, and other research organisms.
Single-cell epigenome profiling is an essential tool for researchers seeking to understand how the epigenome controls cellular identity and function. Common applications include:
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Identifying Regulatory Elements: Mapping cell-type–specific enhancers and promoters in complex tissues.
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Disease Mechanism Studies: Comparing chromatin states between healthy and diseased samples (e.g., cancer, autoimmune disorders, neurodegeneration).
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Developmental Biology: Tracking enhancer activation and chromatin remodeling during cell fate decisions.
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Oncology Research: Profiling tumor heterogeneity to identify subpopulations with distinct regulatory programs.
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Immunology: Linking chromatin accessibility to immune cell activation, tolerance, and exhaustion states.
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Multi-Omic Integration: Using multiome data to directly connect regulatory regions with downstream gene expression changes.
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Drug Development: Assessing epigenetic responses to candidate therapies at single-cell resolution.
What is scATAC-seq Used For?
scATAC-seq with AUGenomics
Sample Submission
Submit viable single-cell suspensions or nuclei. We recommend fresh samples but can work with cryopreserved specimens. Minimum of ~5,000 cells/nuclei required.
Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Typical turnaround for single-cell epigenome profiling projects is 14–21 business days from sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: What’s the difference between scATAC-seq and multiome?
A: scATAC-seq focuses solely on chromatin accessibility, while multiome captures both chromatin accessibility and gene expression from the same cell.
Q: Can I link regulatory elements to specific genes?
A: Yes. We can perform peak-to-gene linkage analysis to connect accessible regions with downstream expression changes
Q: How many cells do I need to submit?
A: We recommend 5,000–10,000 cells per sample to ensure robust coverage, though lower inputs can be accommodated with modified workflows.
Q: How do you link epigenomic data to gene expression?
A: When using the multiome workflow, we integrate chromatin accessibility data with transcriptome measurements to connect open regulatory elements with the genes they control.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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scATAC-seq: Single-cell Assay for Transposase-Accessible Chromatin using sequencing
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Chromatin Accessibility: Openness of DNA regions, indicating potential regulatory activity
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Multiome: Combined measurement of chromatin accessibility (scATAC) and gene expression (scRNA) in the same cell
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Enhancers: DNA elements that boost transcription of target genes
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Nuclei Suspension: A preparation of isolated nuclei used when whole-cell dissociation is not feasible
