Single-Cell ATAC-Seq (scATAC-Seq) Service

End-to-end service to identify open chromatin regions at single-cell resolution


scATAC-Seq Service Overview

Single Cell ATAC-Seq (scATAC) Service

Single Cell ATAC-Seq (scATAC) is based on transposase-mediated insertion of sequencing primers into open chromatin regions. This assay, like traditional ATAC-Seq, provides profiles of open and accessible regions of chromatin that are indicative of active regulatory regions at single cell resolution.

Our scATAC-Seq service enables examination of genome-wide chromatin accessibility of thousands of cells in parallel, allowing examination of subpopulations of cells within a heterogenous population that would otherwise be lost in standard ATAC-Seq.

What are the advantages of using scATAC-Seq?

scATAC-Seq can be used to identify cell subpopulations with different chromatin accessibility profiles within complex samples, eliminating the need for isolation strategies like FACS or magnetic sorting that could alter the biology due to sample manipulation. For example:

  • Identifying cancer stem cells or infiltrating macrophages within a tumor sample
  • Identifying novel cell subpopulations that are responsible for response to drug treatments (i.e. responders vs. resistant cells)
  • Identifying subpopulations of cells with variations in chromatin accessibility that can provide insight into developmental trajectories (i.e. brain development, T-helper cell development, B-cell differentiation)

Learn More About Single-Cell ATAC-Seq

Active Motif's end-to-end scATAC-Seq service includes:

  1. Cell preparation
  2. Transposase reaction
  3. Sample processed using 10X Genomics Chromium platform
  4. Library generation
  5. Sequencing
  6. Bioinformatic analysis

scATAC-Seq Service Data

Single-Cell ATAC-Seq scatter plot

Figure 1: Identify variations in chromatin accessibility across different cell populations within a single sample.

Single Cell ATAC-Seq data generated from mouse kidney tissue. Each color-coded cluster on the tSNE plot represents populations of cells that had the same open chromatin profile. Using this approach, 12 cell populations were identified from a single sample.

Single-Cell ATAC-Seq graph

Figure 2: Analysis of individual cell population using scATAC-Seq can reveal cell subpopulation specific data that would not be captured by “bulk” ATAC-Seq.

Top panel: Representative region from genome-wide “bulk “ATAC-Seq using mouse kidney tissue.
Bottom panel: Same representative region as “bulk” ATAC-Seq from genome-wide scATAC-Seq data. Each cell cluster is displayed as a unique peak track. scATAC-Seq provides the resolution to identify unique open chromatin peak profiles for each cell population, allowing for the identification of cells that are driving a specific phenotype.

Single-Cell ATAC-Seq Webinar

scATAC-Seq Service FAQ

What is single cell ATAC-Seq?

Single Cell ATAC-Seq (scATAC-Seq) allows for the identification of genomic regions that are open/accessible at single cell resolution.

How is scATAC-Seq different from bulk ATAC-Seq?

scATAC-Seq identifies areas of open chromatin at single cell resolution such that when examining a heterogenous cell population it can identify variations in chromatin accessibility between cell subpopulations within a single sample. On the other hand, bulk ATAC-Seq cannot differentiate open chromatin regions or differences in open chromatin among subpopulations within a sample.

Are there any QC steps included in Active Motif’s scATAC-Seq service?

Yes. There are three QC steps that are part of our end-to-end scATAC-Seq service.
  1. After the generation of scATAC-Seq libraries, each library is assessed for quality and proper size using TapeStation or equivalent and quantity is confirmed using qPCR
  2. Shallow sequencing (5-10M reads) and analysis to assess quality metrics (FRIP and number of peaks) prior to deeper sequencing
  3. After full-scale sequencing, there are several numerical and graphical quality metrics assessed during bioinformatics analysis

Is this service specific to human samples?

scATAC-Seq is compatible with both human and mouse samples.

Is scATAC-Seq compatible with FFPE/degraded samples?

No. This assay is not compatible with FFPE as the formalin fixation process can lead to DNA degradation, which can negatively impact the performance as the chromatin structure is not preserved.

How many cells and/or amount of tissue is required for Active Motif’s Single-Cell ATAC-Seq service?

We ask for 250,000 to 2 million cryopreserved cells or 20-50 mg frozen tissue.

What is the read depth for Active Motif’s scATAC-Seq service?

Per 10X Genomics recommendations, we perform ~30,000 read pairs per cell, targeting 5000 cells.


scATAC-Seq Service Documents




scATAC-Seq Service Sample Submission Portal

Our online sample submission portal allows you to easily upload your service project samples and track your project status. Follow the sample submission instructions in the portal to ensure that all your samples arrive at Active Motif in the best possible condition and properly associated with your project.

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