Description

Single-Cell ATAC-seq (scATAC-seq) is a new technology based on the 10x Genomics platform that uses microfluidics and droplet encapsulation techniques to detect open chromatin regions at the single-cell level. It can be used to map single-cell chromatin accessibility and is a high-resolution method for studying the degree of chromatin openness and the regulatory networks of gene expression by DNA-binding proteins. This technology provides an effective means for investigating epigenetics at the single-cell level.

The early research technology for chromatin accessibility is ATAC-seq (Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing). This technique allows for high-throughput sequencing studies of chromatin accessibility (openness). Chromatin open regions are typically loosely packed areas within chromatin where DNA replication and gene transcription occur. ATAC-seq uses modified Tn5 transposase to capture chromatin open regions by introducing sequencing adapters to both ends of the open chromatin, facilitating research in epigenetics and gene regulation.

In 2015, papers published in Science and Nature introduced single-cell ATAC-seq technology for detecting chromatin accessibility and exploring cellular transcriptional regulation mechanisms, addressing previous challenges with cellular heterogeneity and significantly expanding the application range of ATAC-seq technology. In October 2018, 10x Genomics launched the Chromium Single-Cell ATAC Solution, providing a comprehensive and scalable method to analyze chromatin openness in hundreds or thousands of cells from a single sample. This enables multi-omics joint analysis at the single-cell level and in-depth exploration of the epigenetic regulatory mechanisms of cellular heterogeneity.

Technical Principle

Single-cell ATAC-seq involves using modified Tn5 transposase to cut nuclear DNA in a mixed cell nucleus suspension. The nuclei are then encapsulated into droplets using a microfluidic chip, forming a nanometer-scale gel bead emulsion (GEMs). Each cell nucleus's DNA cuts are tagged with a unique 10x barcode. Following library construction and sequencing, the resulting sequences are mapped to individual cell nuclei based on their 10x barcodes.

Advantages

• Low Cost: The cost per cell is significantly lower than traditional single-cell ATAC-seq.
• High Resolution: Detect chromatin accessibility in transcriptional regulatory regions at the single-cell level.
• High Throughput: The 8-channel microfluidic system can capture 500-10,000 cell nuclei per channel in a single run.
• High Efficiency: Achieve a nucleus capture rate of up to 65% per sample.
• Big Data: Obtain data on all chromatin open regions, not limited to specific transcription factor sites.
• Wide Applicability: Suitable for cell lines, primary cells, frozen cells, fresh tissues, and more.
• Extensive Experience: Prepared over 100 tissue types and 5000+ single-cell samples, with extensive experience in high-efficiency nucleus extraction.

Applications

• Chromatin Accessibility Mapping: Mapping open chromatin regions.
• Cellular Heterogeneity: Predicting new cell types based on cellular heterogeneity.
• Epigenetic Modifications in Embryonic Development: Studying epigenetic modifications during embryonic cell development.
• Disease Biomarker Prediction: Predicting potential biomarkers for diseases.
• Tumor Epigenetic Mechanisms: Researching epigenetic mechanisms in tumors.
• Gene Regulation: Investigating gene regulatory mechanisms.