Single-cell ATAC Sequencing

The human DNA chain is about 2m when it is fully unfolded, and needs to be folded into a chromatin structure before it can be stored in the nucleus. The basic structural unit of chromatin is the nucleosome (composed of histone), which refolds to form a highly compressed chromatin structure. The highly folded chromatin structure needs to expose DNA sequences during replication and transcription. This region can be used for the binding of transcription factors and other regulatory elements, so it is closely related to transcriptional regulation. After the compact nucleosome structure is destroyed, the accessibility of cis-regulatory elements such as promoters, enhancers, insulators, silencers, and trans-acting factors is called chromatin accessibility, and this region is called open chromatin or regions of chromatin accessibility.

ATAC-seq (Assay for Transposase-Accessible Chromatin with high throughput sequencing) is a method we use to study chromatin accessibility, which uses the property of the transposase Tn5 to bind open chromatin to capture DNA sequences in open regions, and then obtain the epigenetic research technology of open chromatin regions through high-throughput sequencing. The Tn5 transposase enters and cleaves the exposed DNA regions, and then these regions are connected to a specific sequencing adaptor for high-throughput sequencing, and the sequenced regions are the open chromatin regions.

Chromatin accessibility

ATAC-seq technology

CapitalBio Technology’ Single-cell ATAC sequencing technology utilizes the 10x Genomics single-cell ATAC sequencing platform to detect the open regions of cellular chromatin at the single-cell level. First, the transposase enters the nucleus and preferentially fragments DNA in open regions of chromatin, while adding sequencing primers to the ends of the DNA fragments; secondly, gel beads with barcodes label the DNA fragments in each nucleus in oil droplets, and the DNA with barcode tags is used for subsequent library construction; finally, by sequencing the library on Illumina platform, a large number of single-cell DNA chromatin open region data can be obtained at one time.

In addition to single ATAC assays, 10x Genomics recently introduced single-cell multi-omics technology. After transposase-treated nuclei are encapsulated in oil droplets, special gel beads with barcodes can simultaneously capture DNA and mRNA in the nucleus, enabling combined ATAC and transcriptome detection in the same nucleus.

Experimental workflow for single nucleus ATAC+ RNA

High throughput: Each microfluidic channel can capture 500-10,000 single nuclei at a time

Experimental quality certification: CapitalBio Technology’s Single-cell ATAC Sequencing has obtained the official CSP certificate from 10x Genomics

Single cell omics: Simultaneous detection of gene expression and chromatin open information in the same cell

Multiple sample types: Compatible with cells, fresh tissue, and frozen tissue samples

Conjoint analysis: Transcriptional and chromatin open information combined to provide insights into cell types and epigenetic regulatory mechanisms of key genes

Avoid algorithm errors: Perform joint data analysis directly, without the need to predict the regulation mechanism through the bioinformatics analysis algorithm

scRNA (left) and scATAC (right) cell clustering diagram

scRNA and scATAC cell type correlation

Promoter openness and gene expression difference heatmap

Pseudo-time analysis of scRNA and scATAC

Correlation diagram between gene regulatory elements and target gene expression on a pseudo-time axis

Chromatin co-accessibility analysis

Peak-gene and peak-peak correlation analysis

Development and differentiation

Tumor research

Neuroscience

Disease mechanism