Single-Cell ATAC Sequencing (scATAC-seq) Service

Chromatin accessibility is the "gatekeeper" of the genome. While RNA sequencing tells you what a cell is doing now, Single-Cell ATAC-seq (Assay for Transposase-Accessible Chromatin) reveals what a cell is poised to do next.

By mapping the open chromatin landscape at single-cell resolution, our service allows you to identify cell-specific regulatory elements, transcription factor binding sites, and the underlying circuitry of complex biological systems.

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Submit Your Request Now

Workflow
Deliverables
Biological insights
Why choose
FAQs
Sample preparation

Workflow

scATAC-seq workflow chart

Publication-Ready Deliverables

Every project concludes with a Publication-Ready Data Suite, ensuring you have the visualizations, statistics, and raw files required for submission.

Your Final Data Package Includes:

Standardized Raw Data
High-Resolution Visualizations:
- Clustering & Dimensionality Reduction: UMAP and t-SNE plots identifying distinct cell populations.
- Chromatin Accessibility Tracks: "Genome Browser" style views of specific loci showing differential peak heights across cell types.
- Transcription Factor (TF) Footprinting: Heatmaps and plots showing TF occupancy and motif enrichment.
Rigorous Quality Control (QC) Metrics
Annotated Feature-Barcode Matrices
Methodology Documentation

Biological Insights You Can Reveal

Transcription Factor Profiling: Identify which TFs are driving lineage commitment.
Developmental Trajectories: Map "pseudotime" to see how chromatin closes or opens during differentiation.
Disease Mechanisms: Discover how non-coding "dark matter" mutations impact gene regulation in cancer or autoimmune disorders.

Why Choose Our scATAC-seq Service?

We provide a comprehensive end-to-end workflow—from tissue dissociation to publication-ready insights—using the industry-leading 10x Genomics Chromium platform.
High Sensitivity: Detect rare cell populations and subtle regulatory shifts that bulk ATAC-seq misses.
Regulatory Logic: Link distal enhancers to target promoters to build gene regulatory networks (GRNs).
Cell-Type Discovery: Characterize heterogeneous samples based on their "epigenomic fingerprint" rather than just surface markers.
Expert Analysis: Our bioinformatics team provides more than just raw data; we provide biological context.

FAQs

How many cells/nuclei can be captured per sample?

We typically target capturing 500 to 10,000 nuclei per reaction using the 10x Genomics platform. To ensure we meet this target and account for expected material loss during the isolation and sampling process, we prudently require a starting initial sample of 10^{^6} cells/nuclei.

What is the recommended sequencing depth?

For high-quality publication data, we recommend a minimum of 25,000 to 50,000 raw read pairs per nucleus. This depth ensures sufficient sensitivity to detect rare open chromatin peaks.

Can I combine scATAC-seq with gene expression (RNA-seq)?

Yes! We offer Single-Cell Multiome ATAC + Gene Expression services. This allows you to measure both chromatin accessibility and mRNA from the same single nucleus, providing a direct link between regulatory elements and gene activity.

What bioinformatics pipeline do you use?

Our primary pipeline is based on Cell Ranger ATAC for initial processing, followed by advanced analysis using Signac (R) or ArchR. We can also accommodate custom pipelines if your project requires specific parameters.

Learn about other Q&A.

Sample Submission Guidelines

Sample Type Flexibility: While we accept various formats, flash-frozen tissue or freshly isolated nuclei typically yield the highest signal-to-noise ratios for chromatin accessibility mapping.
Quantity Matters: We require a minimum starting quantity of 5×10⁵ to 1×10⁶ total cells or nuclei per sample. For tissue-based submissions, we recommend providing 20 to 50 mg of flash-frozen material, which provides sufficient biological material for our expert team to perform optimized nuclei extraction while maintaining the chromatin integrity necessary for high-resolution mapping.
No Fixatives: Standard scATAC-seq is incompatible with formaldehyde or PFA-fixed samples.
Purity: Samples must be free of genomic DNA contamination (from lysed cells) and excessive debris, as these will significantly increase background noise in your final publication figures.

Note: Please consult with our experts before preparing your samples to determine the best approach for your project.

* For Research Use Only. Not for use in diagnostic procedures.

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From Our Clients

"I recently used their proteomics service for a project analyzing protein interactions in yeast models. The team was very responsive and helped clarify the methodology they employed, which made me feel confident in the results. The data quality was solid, with clear identification of several key proteins involved in our study. Their thorough analysis enabled me to pinpoint specific interactions that I hadn't considered before, which significantly improved the direction of my research. I appreciate their professionalism and support throughout the process."

Sarah Thompson, University of California, Berkeley

"Our lab collaborated with them on a project studying cancer biomarkers. The proteomics analysis provided was detailed and focused, specifically highlighting the differential expression of proteins between healthy and tumor samples. Their clear explanations of the data helped my team understand the biological implications. I also appreciated their willingness to revise the reports based on our feedback, ensuring that we had everything we needed for our publication. This collaborative spirit was invaluable."

Emily Rodriguez, Stanford University

"Our lab worked with them on a project studying the effects of diet on gut microbiota using proteomics. They used a label-free quantification method to analyze proteins in fecal samples before and after dietary intervention. The results showed significant changes in protein expression linked to microbial activity. This was pivotal for our hypothesis about diet-microbiota interactions. The clarity of their data presentation made it easy for our team to integrate these findings into our ongoing research."

Dr. Lisa Wong, University of Toronto

"My experience with Creative Proteomics during the mass spectrometry analysis was excellent. We sent in human saliva and mouse brain tissue samples, which they expertly analyzed using both LC-MS and GC-MS techniques. The results were invaluable, revealing key metabolites in the saliva and identifying biomarkers linked to brain function in the brain tissue."

Dr. Emily Carter, Senior Research Scientist

"The overall service from Creative Proteomics was outstanding. They made the entire process seamless and efficient, allowing us to focus on our research. We worked with leaf and root samples from various Arabidopsis genotypes for targeted metabolomics analysis. Their thorough profiling of primary and secondary metabolites gave us important insights into how the plants respond metabolically to environmental stress."

Dr. Laura Henderson, Plant Physiologist

"We had a pleasant collaboration with Creative Proteomics on mass spectrometry analysis of lipids. They conducted a detailed analysis of lipid species, providing us with important insights into lipid metabolism and its relationship with metabolic syndrome disease states."

Dr. Sarah Mitchell, Research Scientist

Online Inquiry

Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to for inquiries.

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