InquirySingle-cell ATAC Sequencing (scATAC-seq) is a novel technology based on microfluidics and oil droplet encapsulation technology using the 10x genomics platform. It reveals the accessibility of single-cell chromatin, distinguishes cellular heterogeneity, and obtains information such as the open chromatin regions, transcription factor binding states, regulatory regions of nucleosomes, and chromatin states. Hence, scATAC-seq is an important breakthrough in single-cell epigenetics.
Principle of scATAC-seq
First, the nucleus suspension is incubated with a modified Tn5 transposase mixture to enter the nucleus, preferentially cleaves the open chromatin region to induce DNA fragmentation, and adds sequencing primers to the ends of the DNA fragments. Then, the gel bead with tag (Barcode) and nucleus are wrapped in an oil droplet to form the nanoscale gel microbead emulsion (GEM). Subsequently, gel beads are lysed, and the nuclei are cleaved to release DNA fragments that are tagged with Barcodes at the end. Upon the rupture of GEMs, tagged DNAs are recovered, and the library is constructed. Finally, the library is sequenced using the high throughput Illumina sequencing platform. As a result, obtained sequences that are associated with each individual nucleus are sorted using the 10x Barcode.
Our End-to-end scATAC-Seq Service
Our scATAC-Seq service enables examination of genome-wide chromatin accessibility of thousands of cells in parallel and allows examination of subpopulations of cells within a heterogeneous population that would otherwise be lost in standard ATAC-Seq.
Our end-to-end scATAC-Seq service includes:
Bioinformatics Analysis
Applications
1. Discovery of cellular heterogeneity caused by epigenetic variations
2. Construction of gene regulatory networks upstream of gene expression
3. Defining cell types and differentiation states
4. Predicting molecular markers of diseases
Sample Requirements
Species requirements: human, mouse, and other species with higher genome quality required
Sample type: single cell or nucleus suspension, total cells numbers in cell suspension should be greater than 105;
Cell types: cell lines, primary cells, cryopreserved samples
Cell activity: the proportion of viable cells should be greater than 70%
Size of nucleus: less than 40 μm in diameter, with good nuclear membrane integrity and the more than 95% nucleus proportions
Advantages
1. Real single-cell sequencing: Real single-cell sequencing is realized through the oil droplet-barcode-single cell correspondence;
2. High cell capture efficiency: the capture efficiency of a single cell is as high as 65%, which can accurately identify rare cell types;
3. Wide compatibility of sequencing platforms: highly compatible with various Illumina platforms;
4. Cost-effective: Compared with other single-cell platforms, it is simple operated and cost-effective;
5. Ultra-high throughput: the number of cells detected in a single sample ranges from 1,000 to 10,000;
6. Rich experience in the preparation of multi-species and multi-tissue types of single-cell suspensions;
7. Provide personalized analysis:
a. Epigenomic studies at single-cell resolution
b. Open chromatin regions analysis and visualization for single cell
FAQ
1. How to choose scATAC-seq data?
It is recommended to measure 25,000 read pairs per nucleus and 25~50 G data volume to achieve the best sequencing data volume and sequencing saturation generally.
2. What are the differences between scATAC-seq cell fractionation and scRNA-seq?
Single-cell ATAC sequencing clusters cells based on chromatin accessibility and obtained cell clusters are not dependent on gene expression, which is more sensitive for low-abundance expressed cells and suitable for the study of low-abundance expressed cells through open chromatin regions.
3. Can scRNA-seq be combined with scATAC-seq?
Yes.
Currently, two cases have combined the analysis of scRNA-seq with scATAC-seq.
(1) With sufficient cell volume, a single cell suspension can be divided into two portions for 10X scRNA and 10X scATAC, respectively, after nucleation. scRNA-seq and scATAC-seq can be performed separately, and combined analysis can be performed to explore more gene regulatory networks with epigenetic potential based on chromatin accessibility and gene expression.
(2) The latest single-cell multi-omics solution from 10x Genomics: Chromium single-cell multi-omics ATAC+ gene expression, which realizes the simultaneous analysis of gene expression and open chromatin in the same cell and will obtain ATAC library and gene expression library sequencing raw data loading into the Cell Ranger ARC analysis pipeline and visualized with Loupe Browser to correlate gene expression reads with potential regulatory functions. The relationship between chromatin openness and gene expression obtained is more closely and objectively realistic, which helps find the relationship between gene expression regulation.
