ATAC Sequencing

Assays for Transposase-Accessible Chromatin using sequencing, short for ATAC-Seq, is a next-generation sequencing (NGS)-based method to study the open regions of chromatin on a genome-wide scale. ATAC-Seq has the advantages of easy operation, no crosslinking required, high signal-to-noise ratio, and low requirement for sample amount. Combined the data of ATAC-Seq, RNA-Seq, and epigenomics, the relationship between gene differential expression and regulation can be studied more accurately and comprehensively.

Overview

The DNA of eukaryotes is tightly bound to a group of proteins called histones, which constitute half the mass of a eukaryotic chromosome. There are numerous units that DNA enwinds histone formed a bead like structure called nucleosome, and the chromatin looks like many beads on a string. DNA replication and gene transcription require the unwinding of the higher structure of DNA. Open chromatin regions are these folded regions that contain important binding sites for transcription factors and transcriptional regulatory elements. ATAC-Seq utilizes the hyperactive mutant Tn5 transposase to insert sequencing adapters into accessible DNA regions, through which the open chromatin sequence can be separated from the entire chromatin, followed by next-generation sequencing and corresponding bioinformatics analysis. The research on open chromatin addresses the needs for deeper understanding of gene regulation, transcription factors that relate to cell physiology and diseases, etc.

Project Workflow

Bioinformatics Analysis Pipeline

In-depth data analysis:

• Data quality control;
• Peak calling and annotation;
• Fragment size distribution;
• Gene ontologies;
• KEGG pathways;
• Differential analysis.

Sample Requirements

Cell sample ≥ 50,000 cells; Nucleus sample ≥ 50,000 nuclei

Sample storage: Nuclei can be frozen at –20˚C for up to two days, avoid repeated freezing and thawing.

Shipping Method: Samples are supposed to stored in a 1.5 mL microcentrifuge tube, sealed with sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, full statistical analysis & alignments, custom analysis reports on customer request.

References:

1. Satpathy AT, Saligrama N, Buenrostro JD, et al. Transcript-indexed ATAC-seq for precision immune profiling. Nature medicine. 2018;24(5):580-90.
2. Divate M, Cheung E. GUAVA: a Graphical User Interface for the Analysis and Visualization of ATAC-seq Data. Frontiers in genetics. 2018;9:250.
3. Corces MR, Trevino AE, Hamilton EG, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods. 2017;14(10):959-62.
4. Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC‐seq: a method for assaying chromatin accessibility genome‐wide. Curr Protoc Mol Biol. 2015;109(1):21.9. 1-.9. 9.