Single-cell ATAC Sequencing CapitalBiotech

The human DNA chain is about 2 meters in lenght 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 proteins, which refolds to form a highly compressed chromatin structure. The highly folded chromatin structure must expose DNA sequences during replication and transcription. This region can be used for the binding of transcription factors and other regulatory elements, which 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 used study chromatin accessibility, which leverages 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 exposed DNA regions, which are then connected to a specific sequencing adaptor for high-throughput sequencing, and the sequenced regions are the open chromatin regions.

Chromatin accessibility

ATAC-seq technology

CapitalBiotech's 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, transposase enters the nucleus and preferentially fragments DNA in open regions of chromatin, simultaneously adding sequencing primers to the ends of the DNA fragments. Second, gel beads with barcodes label DNA fragments from each nucleus within oil droplets, and the DNA with barcode tags is used for subsequent library construction. Finally, by sequencing the library on an Illumina platform, a large scale of single-cell DNA chromatin open region data can be obtained in one run.

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 from the nucleus, enabling combined ATAC and transcriptome detection within the same nucleus.

Experimental workflow for single nucleus ATAC+ RNA

High throughput: Each microfluidic channel can capture 500-10,000 single nuclei per run

Experimental quality certification: CapitalBio Technology’s Single-cell ATAC Sequencing is officially CSP-certified by 10x Genomics

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

Multiple sample types: Compatible with single cells, fresh tissues, 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