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:
- Cell preparation
- Transposase reaction
- Sample processed using 10X Genomics Chromium platform
- Library generation
- Bioinformatic analysis
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.
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.
How is scATAC-Seq different from bulk ATAC-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.
- 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
- Shallow sequencing (5-10M reads) and analysis to assess quality metrics (FRIP and number of peaks) prior to deeper sequencing
- 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 tissue is recommended for Active Motif's scATAC-Seq service?
The amount of cells and/or tissue recommended for our scATAC-Seq service is highly dependent on the cell and tissue type. We recommend first consulting with your key account manager to discuss your project. Click here
to locate your key account manager.
What is the read depth for Active Motif’s scATAC-Seq service?
Per 10X Genomics recommendations, we perform at least 30,000 read pairs per cell. We target 5000 cells, achieving a range of 3000 to 7000 cells.
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