Epigenome Sequencing

Single Cell ATAC-Seq

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Single Cell (ATAC-Seq) Services

Genome-wide profiling of open chromatin regions

Single cell (ATAC-Seq) services provide detail insights into cell type heterogeneity, gene regulation and their developmental pathways.

The scATAC-seq (Single Cell Assay for Transposase-Accessible Chromatin using sequencing) technique unveils the open chromatic landscape within individual cells. By inserting transposase-mediated sequencing primers, scATAC-seq maps active regulatory regions with remarkable single-cell precision. This powerful method allows researchers to investigate diverse cell subpopulations at a single cell resolution. At SeqMatic, this approach is making impressive strides in diverse research areas, including cancer cell investigations, the discovery of novel cell subpopulations in response to drug treatments, and the study of critical developmental processes such as brain maturation and B-cell differentiation. One popular application is to assess exhaustion in CAR-T and other engineered immune cells.

SeqMatic offers 10x Genomics single cell ATAC-seq and multiome.

Available Run Types:

10x Genomics can process:

Up to 20K cells per sample (1-8 samples) using Chromium Epi Chromatin kit

Service Features

Stringent Quality Controls – Your single cell submissions are assessed with Countess II to quantify cell concentration in suspension and cell viability before Chromium processing. Working carefully with your SeqMatic team to prepare your submission ensures superior cell recovery and GEM formation.

Scientific considerations for read depth – SeqMatic recommends a read depth of 25K read pairs per nucleus (50K individual reads; 25K from R1, 25K from R2). Higher and lower read depths are available depending on model organism requirements and/or project needs.

Preliminary Sequencing – After library preparation, SeqMatic prepared libraries are pooled to customer requirements and the final QC is checked via preliminary sequencing. Libraries are then normalized and re-pooled based on the nuclei count from the preliminary sequencing dataset.

World-class validation standard & practices – SeqMatic is equipped to ensure accurate, repeatable and reproducible results. SeqMatic’s quality program has been audited and approved as part of becoming a Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP) certified sequencing facility. Our CLIA quality program requires the use of well-defined protocols to maintain the consistency and reproducibility of our NGS workflows. Thus, the samples will be processed in a CLIA environment.

Custom assay services – Our highly personalized sequencing services can be adapted to almost any (high and/or low throughput) sequencing workflow required by our customers so that we optimize the quality and quantity of data output.

Service Highlights

Comprehensive Services

Single cell ATAC workflow services include nuclei extraction, tagmentation and library generation, single cell barcoding, library amplification and sequencing, and a full suite of bioinformatics support.

Expert Volume Handling

From small projects with a few samples or low input to large scale high-throughput projects

Wide Range of Sample Types
Human, animal, plant, fish, etc.
Fresh/frozen cells and tissue samples

Bioinformatics
Full suite of custom and 10x Genomics analytic pipelines (Cell Ranger) available for individual project needs
Comprehensive Cell Ranger ARC report is available as part of SeqMatic’s standard bioinformatics pipeline