ATAC-seq Services: End-to-End Chromatin Accessibility Profiling

Epigenome Technologies provides end-to-end ATAC-seq services covering library prep, sequencing, and bioinformatics for fresh or frozen tissues and cryopreserved cells, yielding detailed genome-wide maps of open chromatin.

High-resolution chromatin maps

Deep, biologically informative profiles

Capture promoter, enhancer, and TF motif accessibility with optimized chemistry.

Reliable Performance Across Cohorts

Consistent results, sample to sample

Protocols refined to support reproducible signal quality across fresh, frozen, and cryopreserved materials.

Scientist-Led Support

Guidance at every step

From study design to data review, dedicated scientists collaborate with you throughout the program.

Speak with a Scientist Request a Project Brief Get a Quote

ATAC-seq for Open Chromatin and Regulatory Element Discovery

Genome browser tracks of ATAC-seq chromatin accessibility in normal and KO/CKO HeLa cells
Example ATAC-seq from normal and KO/CKO HeLa cells.

ATAC-seq profiles chromatin accessibility at base-pair resolution, surfacing which regulatory elements (such as promoters, enhancers, and other cis-regulatory elements) are exposed to binding by proteins such as transcription factors or polymerase. From samples to figures, this turnkey ATAC-seq service handles library prep, sequencing, and bioinformatics, delivering ready-to-use maps of open chromatin and differential accessibility across your cohorts.

Key ATAC-seq Applications

  • Mechanistic oncology and immunology studies that benefit from enhancer-level resolution.
  • Developmental or disease cohorts with scarce material or shifts in regulatory landscape.
  • CRISPR, degrader, and perturbation screens validating on-target chromatin outcomes.
  • Cell and gene therapy programs: monitor regulatory state in CAR‑T across discovery and optimization.

ATAC-seq Collaboration Model

  • Joint design sessions align sample availability, replicates, sequencing depth, and effective controls.
  • Project scientists remain embedded through QC reviews, data processing, and interpretation.
  • Bioinformatic integration of ATAC with RNA, CUT&Tag, or third-party datasets on request.

Downstream ATAC-seq Analysis

  • Motif discovery and regulatory annotation for differential peaks.
  • Promoter and enhancer linkage summaries for translational storytelling.
  • Actionable slide-ready visualizations delivered alongside raw outputs.
The ATAC-seq service was a really useful addition to the ChIP-seq: looking at occupancy with respect to open chromatin has been a big deal for this project. Bundling the ATAC service with ChIP made it very cost-effetive for us.

Post-doctoral researcher, NYIT

ATAC-seq Workflow and Checkpoints

  1. Plan

    We confirm sample condition, spike-ins, sequencing depth, and optional multiomic deliverables before kickoff.

  2. Prepare & construct

    Nuclei isolation and ATAC chemistry with QC on fragment ladders, complexity, and transposition efficiency.

  3. Sequence

    Paired-end runs on AVITI, NovaSeq, or NextSeq platforms with lane balancing against internal standards.

  4. Interpret

    Automated alignment peak calling, motif enrichment, and data packages aligned to your preferred analysis environment.

Genome browser view of reproducible ATAC-seq accessibility changes across four perturbation conditions
Highly-reproducible ATAC-seq studies show clear differences in regulatory accessibility in perturbation studies

Operational cadence

  • Day 5 nuclei and library QC review with your project scientist.
  • Day 10 library acceptance with fragment distribution and concentration reports.
  • Day 14 FASTQ and peak delivery.
Illustration of ATAC-seq sample intake timeline
Milestones from sample receipt through analysis-ready reporting.
Schedule Project Kickoff Request ATAC-seq Sample Prep Checklist

Platinum-quality Chromatin Accessibility

  • FRiP distribution summaries with cohort medians and percentile bands.
  • TSS enrichment overlays compared directly to ENCODE guidance for every sample.
  • Insert-size and nucleosome ladder plots reviewed prior to sequencing approval.
  • Peak concordance against ENCODE DNase-seq and your internal reference datasets.

ATAC-seq Delivery Package

  • Sequencing-ready libraries with concentration, laddering, and complexity documentation.
  • FASTQ, peak sets, and metadata formatted for immediate cloud or on-prem ingestion.
  • Interpretive report summarizing differential accessibility, pathway context, and recommended next steps.
Request Data Package Example
Composite QC dashboard illustrating FRiP distribution, TSS enrichment traces, and insert size histogram for ATAC-seq runs
QC dashboards highlight FRiP, TSS enrichment, and insert-size performance per run.
ATAC-seq TSS enrichment and replicate correlation heatmap
TSS enrichment and replicate correlation heatmaps benchmarked to ENCODE thresholds.
Genome browser comparison of Epigenome Technologies ATAC-seq peaks versus ENCODE DNase-seq benchmark tracks
Genome browser overlays comparing Epigenome Technologies peaks to ENCODE DNase-seq references.
Deliverable Summary SLA
Sequencing-ready libraries Fragment distribution, concentration, and QC documentation. Day 10
FASTQ and peak files Aligned reads, narrowPeak/broadPeak outputs, ENCODE-compliant metadata. Day 14
Interpretive report Motif enrichment, differential accessibility, and pathway overlays. Day 16

Partner with our scientists

Share your targets, cohort size, and required timelines. We will return a scoped ATAC-seq brief outlining assay mix, QC checkpoints, and downstream reporting.

  • Sample requirements: 75K nuclei preferred with low-input contingencies available.
  • Storage guidance: Fresh, cryopreserved, or FFPE submissions accepted with documented handling.
  • Data options: Raw, processed, and interpretive outputs available individually or bundled.
  • Support: Project scientists provide experimental planning and guidance, data reviews, and troubleshooting.
Start an ATAC-seq Project Email the ATAC-seq Team