How does Creative Biolabs handle high mitochondrial DNA contamination in cancer cells?

We utilize the omni-ATAC protocol, which incorporates specialized detergents and washing steps to keep mitochondria intact while selectively lysing the plasma membrane. This ensures that the Tn5 transposase primarily targets nuclear DNA.

Can you perform ATAC-seq on snap-frozen tumor tissues?

Yes. We have optimized single-nucleus ATAC-seq (snATAC-seq) protocols specifically for frozen tissues, allowing us to capture the chromatin state even when intact live cells are unavailable.

How does ATAC-seq complement my existing RNA-seq data?

While RNA-seq tells you which genes are expressed, ATAC-seq tells you why—identifying the specific enhancers and TFs that are physically driving that expression.

ATAC-seq based Chromatin Accessibility Mapping Service

Creative Biolabs provides a comprehensive analytical platform to transform complex biological specimens into actionable epigenetic blueprints. By utilizing high-resolution ATAC-seq, we identify the "regulome"—the active enhancers, promoters, and insulators defining the malignant state. We pinpoint specific transcription factor (TF) binding sites and structural shifts driving epithelial-to-mesenchymal transition (EMT), hypoxia, and therapeutic resistance. Our deep-dive analysis links genetic mutations (e.g., KRAS, TP53) to the chromatin landscape, identifying how non-coding variants function within specific lineages to resolve the "master switches" of cancer cell fate.

The Power of ATAC-seq in Cancer Research

ATAC-seq has revolutionized regulome mapping by utilizing hyperactive Tn5 transposase to probe active enhancers, promoters, and transcription factor footprints. As highlighted in recent benchmarks, it outperforms traditional methods through minimal sample requirements; our Omni-ATAC workflow achieves superior results with fewer than 50,000 cells, ideal for precious clinical biopsies. Unlike ChIP-seq, ATAC-seq provides agnostic, unbiased profiling of the global regulatory landscape without a priori target knowledge. By integrating tagmentation, we ensure rapid scalability for large patient cohorts, effectively bridging the gap between benchtop discovery and high-throughput diagnostic pipelines.

Key Deliverables and Solutions

To ensure the success of your cancer research, Creative Biolabs offers a modular and highly customizable suite of ATAC-seq solutions. Our offerings are designed to meet the rigorous demands of fundamental research and biopharmaceutical development:

Standard & Omni-ATAC Mapping

Creative Biolabs provides high-fidelity mapping of open chromatin regions using specialized protocols. Our Omni-ATAC chemistry significantly minimizes mitochondrial DNA interference, maximizing sequencing depth and sensitivity for identifying active enhancers and promoters in precious clinical specimens.

Single-Nucleus ATAC-seq (snATAC-seq)

Resolve epigenetic heterogeneity within complex tumor microenvironments. Our snATAC-seq platform enables the precise separation of malignant cells from stromal and immune infiltrates, uncovering rare cell states and drug-resistant subpopulations invisible to bulk sequencing.

Multi-Omic Co-Profiling

Establish direct regulatory links by simultaneously assessing chromatin accessibility and gene expression from the same nucleus. Our snATAC + snRNA-seq co-profiling provides a comprehensive view of how epigenetic "switches" drive specific transcriptomic outputs.

Advanced Bioinformatics Suite

Our suite features TF footprinting to identify physical protein-DNA interactions. We provide nucleosome positioning analysis and distal enhancer-to-gene peak linking to map the complex regulatory architecture of the cancer genome.

Custom Research Pilot Studies

We offer tailored optimization for rare or difficult specimens, including fine-needle aspirates (FNA) and liquid-derived cancer cells. Our experts design custom pilot studies to ensure robust data generation from low-input or highly fragmented archival clinical materials.

Workflow

Our ATAC-seq workflow is optimized for transparency, reproducibility, and high signal-to-noise ratios even in difficult research samples.

Publication

ATACgraph is a comprehensive bioinformatics toolkit specifically designed for analyzing ATAC-seq data. It enables genome-wide chromatin accessibility profiling, identification of nucleosome-free and occupied regions, and detection of differentially accessible regions. Integrating quality control and visualization features, it offers a user-friendly interface via the Galaxy platform alongside a command-line option. This tool allows biologists to efficiently interpret chromatin dynamics and integrate ATAC-seq with other sequencing data like ChIP-seq and RNA-seq.

Why Choose Us?

Creative Biolabs stands at the forefront of epigenetic innovation by offering the omni-ATAC protocol as a standard. One of the primary bottlenecks in cancer ATAC-seq is mitochondrial DNA (mtDNA) contamination, which can consume up to 80% of sequencing reads. Our proprietary optimization reduces mtDNA read waste by up to 70%, drastically increasing the effective depth for nuclear regulatory regions. Our expertise is grounded in Published Data demonstrating high-resolution mapping across 11+ tumor types, including pancreatic, lung, and breast cancers. By choosing Creative Biolabs, you gain access to a platform that can deconvolute signals from complex tumor microenvironments, identifying cell-type-specific regulatory programs that traditional bulk methods overlook.

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How to Contact Creative Biolabs

Creative Biolabs offers an end-to-end ATAC-seq mapping service that combines high-sensitivity wet-lab protocols with expert bioinformatic analysis. We are committed to helping you decode the complex regulatory networks of cancer to identify the next generation of therapeutic targets.