Single-cell ATAC-seq
Epigenomic information provides greater insight into gene regulation, but is complicated by the fact that individual cells (even those of the same type) may have distinct epigenomes. Our ICELL8 platform offers a high-throughput solution that enables the generation of single-cell ATAC-seq (scATAC-seq) libraries from >1,000 cells in a 4–5-hour on-chip automated workflow.
Epigenomic information provides greater insight into gene regulation, but is complicated by the fact that individual cells (even those of the same type) may have distinct epigenomes. Our ICELL8 platform offers a high-throughput solution that enables the generation of single-cell ATAC-seq (scATAC-seq) libraries from >1,000 cells in a 4–5-hour on-chip automated workflow.
ATAC-seq: generate genome-wide chromatin accessibility maps
ATAC-seq stands for Assay for Transposase-Accessible Chromatin using sequencing. ATAC-seq is used for the genome-wide mapping of chromatin accessibility and employs a hyperactive Tn5 transposase to selectively insert DNA adapters into accessible chromatin loci. Adapter-ligated DNA fragments are then amplified by PCR and used to generate sequencing-ready libraries. This method represents a powerful tool for investigating the dynamics of gene expression regulation and allows for the simultaneous examination of the accessibility of genomic DNA to transcription factors and nucleosome position(s) in regulatory sites, while providing a genome-wide map of chromatin accessibility.
ATAC-seq on the ICELL8 platform
Our ICELL8 platform enables a simple, relatively inexpensive scATAC-seq workflow that offers a 20-fold increase in throughput compared to prior methods. Our technology allows the generation of ATAC-seq data from >1,000 viable cells isolated and selected automatically with the ICELL8 Single-Cell System (Cat. No. 640000) and CellSelect Software. The chip is then transferred to the ICELL8 Chip Cycler where tagmentation, indexing, and PCR amplification is performed on-chip. Following amplification, full-length amplicons are pooled off-chip, purified, and the purified cDNA is amplified to yield the final sequencing-ready libraries.
Overview
- High library complexity—more than 13,000 unique fragments per single cell
- Good signal-to-noise ratio—greater than 10-fold enrichment of desired reads at transcriptional start sites
- Robust clustering—application data with PBMCs demonstrates robust clustering of B, T, and monocyte cells
More Information
Applications
- High-throughput scATAC-seq library generation for Illumina platforms
- Nucleosome mapping
- Determination of transcription factor occupancy
Components
The following items are required to complete the workflow:
| ICELL8 Single-Cell System (Cat. # 640000) | ||
|---|---|---|
| Cat. # | Product | 1 item required per: |
| 640196 | ICELL8 Blank Chip Reagent Kit | 1 chip |
| 640183 | ICELL8 250v Chip | 1 run |
| 640048 | ICELL8 Collection Kit | 1 chip |
| 640018 | MSND 384-Well Source Plate and Seals* (20/pack) | 4 chips |
| 640037 | MSND 384-Well Source Plate and Seals* (120/pack) | 24 chips |
| Additional Takara Bio reagents required for the protocol: | ||
| RF001A | e2TAK DNA Polymerase | |
| 639132 | Advantage UltraPure dNTP Combination Kit (100 mM each dNTP) | |
*Note: Cat. No. 640018 contains enough plates and film for 4 chips. If you plan on processing more chips, Cat. No. 640037 has enough plates and sealing film for up to 24 chips.
Additional product information
Please see the product′s Certificate of Analysis for information about storage conditions, product components, and technical specifications. Please see the Kit Components List to determine kit components. Certificates of Analysis and Kit Components Lists are located under the Documents tab.
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