ATAC-Seq Frequently Asked Questions

Review our ATAC-Seq Best Practices for sample submission.

General Questions

1. What type of samples can I submit?

We accept cryopreserved cells, frozen plant tissue, and Illumina®-compatible premade libraries for sequencing (see our sample submission guidelines below. To promote delivery of high-quality data for cyropreserved cells, we ask customers to provide 3 tubes per sample with 100,000-200,000 cells and >90% viability for ATAC-Seq library preparation. If your sample has less than 100,000 cells, a member of our team can discuss options for your project. See our sample processing workflow for more details. Please feel free to contact us.

2. How do I prepare my own libraries for sequencing?

You can use any Illumina-compatible ATAC-Seq library preparation kit. Please see our Sequencing Only FAQs for additional library preparation guidelines.

3. Is data analysis available?

Yes, our standard ATAC-Seq data analysis includes alignment to a reference sequence, peak calling, and differential analysis. We also have an integrated data analysis pipeline with RNA-Seq. Custom analysis is also available upon request.

4. Can RNA-Seq be performed on the same ATAC-Seq samples?

Yes, Azenta Life Sciences is testing a proprietary workflow for parallel nuclei isolation, library preparation, sequencing, and integrated data analysis for ATAC-Seq and RNA-Seq from the same cells.

5. Does Azenta Life Sciences offer single-cell ATAC-Seq?

Azenta Life Sciences is also testing a proprietary workflow for ATAC-Seq on single-cell samples using the 10x Genomics Chromium system. If you are interested in this service, please contact us.

6. How do I contact Azenta Life Sciences for a technical consultation about my project?

Please submit an inquiry here. Azenta's NGS team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation.

7. Can you recommend the best data delivery option?

Yes, we can recommend the best data delivery option based on the platform and project details. Options include

  • Secure File Transfer Protocol (sFTP)
  • Customer cloud account
  • Hard drive (additional charges may apply)

8. How will my data be delivered?

If your results are being shipped to you via hard drive, you can track its shipment using the tracking number provided to you in the delivery email sent from Azenta.

If your results are being delivered via another data delivery method, such as AWS S3, Aspera, or other cloud-based methods, please refer to the delivery email sent from Azenta for detailed information on the transfer, and consult with your IT department to ensure compliance with your institution’s policies.

If your results are being sent via a secure File Transfer Protocol (sFTP), please refer to Azenta's sFTP Data Download Guide for instructions on how to download your data and troubleshooting tips.

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Sample Preparation

9. How should I prepare and send my samples?

Sample Type: Cryopreserved Cells

Recommended Amount: 3 tubes of >500,000 cells in 500 μL each

Minimum Amount: 3 tubes of 100,000 cells in 500 µL each (less can be accepted if necessary; please inquire)

Buffer: Cryopreservation media (e.g. cell culture media supplemented with 10% DMSO)

Shipment Method: Dry ice

Sample Type: Frozen Plant Tissue

Amount: Very little frozen tissue is required; the equivalent of a microcentrifuge tube filled with tissue should be sufficient

Note: Samples cannot be submitted in solution, such as RNAlater.

Shipment Method: Dry ice


Sample Type: Premade Sequencing Library

Recommended Amount: >15 nM, >20 µL

Buffer: Water, EB, or low TE (<0.1 mM EDTA)>

Shipment Method: Dry ice

Ship samples directly to our facility. Use the shipping address listed on the order receipt.

10. What happens if my samples do not meet your starting material requirements?

Please contact us.

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Order & Processing

11. How do I request a quote?

For a quick tutorial, watch the video below.

  • For ATAC-Seq library preparation and sequencing, select the Epigenomics icon and then ATAC-Seq.
  • For sequencing of premade ATAC libraries, select the Sequencing Only icon.

12. How do I confirm a quote?

For a quick tutorial, watch the video below.

13. How do I submit the Azenta sample form (to provide detailed information about my samples)?

For a quick tutorial, watch the video below.

14. How can I monitor the progress of my project?

The status of your order, including an estimated date of delivery, can be viewed anytime through your Azenta account. Visit the Order Summary page of your project to find the current order status.

15. How long do you hold samples?

We hold samples for 1 year after project completion. Please contact us if you would like samples retained for a longer period of time or shipped back to you.

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