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, 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 reach out to us (see contact information at the bottom of the page).

 

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, GENEWIZ 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 GENEWIZ offer single-cell ATAC-Seq?

GENEWIZ 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 inquire (see contact information below).

 

6. How do I contact GENEWIZ for a technical consultation about my project?

GENEWIZ's NGS team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation. Contact us (see below).

 

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)

 

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Sample Preparation

 

8. How should I prepare and send my samples?

Sample Type: Cryopreserved Cells

Recommended Amount: 3 tubes of >200,000 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.

 

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

Please contact us (see information at the bottom of the page).

  

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Order & Processing

 

10. 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.

 

11. How do I confirm a quote?

For a quick tutorial, watch the video below.

 

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

For a quick tutorial, watch the video below. 

 

13. 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 GENEWIZ account. Visit the Order Summary page of your project to find the current order status.

 

14. 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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Have a specific question?

North & South America: Email |  Phone 1-877-436-3949, Ext. 1

Europe: Email |  Phone +49 341 520 122-41

 

 

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