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Single-Cell ATAC-Seq:
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Questions? Please contact our Next Generation Sequencing (NGS) team at NGS@genewiz.com or toll-free at 877-436-3949 ext. 1.

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Frequently Asked Questions


ATAC-Seq is a bulk sequencing technology used to assess genome-wide chromatin accessibility. One caveat with bulk ATAC-Seq is that the chromatin signal is averaged for all cells in a sample, limiting insights into low-abundance phenotypes or rare populations of cells. Single-cell ATAC-Se(scATAC-Seq) enables researchers to interrogate the chromatin landscape of hundreds to thousands of individual cells at the single-cell level.

Ordering & Sample Preparation

Absolutely! GENEWIZ's NGS team, a group of dedicated technical experts, is available to assist with designing your experiment and answering any questions you may have. You can submit your questions using the quote request form to your left, or you can submit an inquiry through the button above. 

Sample Type: Cryopreserved single-cell suspension according to GENEWIZ-supplied protocol, submitted in duplicate. 

Recommended Amount: >1E6 cells in 1 mL

Minimum Amount: 100,000 cells in 500 µL (Note: 1E6 cells are required for dead cell removal)

Buffer: Cryopreservation media (e.g. cell culture media supplemented with 20% FBS and 10% DMSO)

Note: GENEWIZ has developed a proprietary cryopreservation protocol to aid shipment of samples. You can learn more about our protocol here.

Our workflow is illustrated hereTo ensure the highest-quality data, viability and cell counts are measured immediately upon sample receipt, as cells must be processed on the 10x Genomics® ChromiumTM Controller as soon as possible. As such, we developed a predefined workflow when samples do not pass the initial QC for viability or cell count. 

If you answer "No" to the question "Do you authorize sample processing according to our workflow?" in your quote request, we will not process samples that fail QC until receiving your consent. We will always contact you with any issues regarding your samples; however, please keep in mind that delays in communication can severely impact sample quality.


We use the 10x Genomics® ChromiumTM Controller coupled with Illumina® NGS sequencing. The Chromium Controller uses a microfluidic chip that partitions cells across tens of thousands of Gel Beads-In-Emulsion (GEMs). This combination allows researchers to bioinformatically identify reads from hundreds to thousands of single cells in high-throughput fashion. 10x scATAC libraries use paired-end sequencing and dual indexing with the following configuration:

  • Read 1: 50 cycles
  • i7 Index: 8 cycles
  • i5 Index: 16 cycles
  • Read 2: 50 cycles

The number of reads required depends upon genome size, number of known genes, cell type, and chromatin status of a sample. For most applications, 50,000 read pairs is the minimum read depth for scATAC-Seq (25,000 read 1, 25,000 read 2). We recommend 75,000 total reads per cell to maximize the identification of open chromatin regions in each cell.

Data Analysis & Delivery

GENEWIZ will recommend the best data delivery option based on the platform and project details. Data delivery options include:

  • Secure File Transfer Protocol (SFTP)
  • Customer Cloud account
  • Hard drive (additional charges may apply)

Please mention in the Additional Comments section of your quote request if you have any specific preference for the above options.


GENEWIZ’s next generation sequencing services deliver an unmatched combination of quality, reliability, and expertise. We have spent years optimizing our processes to deliver the highest-quality results that meet your budget and deadline. 


View more reasons to choose GENEWIZ.