Chromium Single Cell ATAC
Reveal the Epigenomic Landscape, Cell by Cell
Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin) allows you to analyze chromatin accessibility at the single cell level, providing insights into cell types and states, and deeper understanding of gene regulatory mechanisms.
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Detect chromatin accessibility
Analyze thousands of unique open chromatin fragments per cell, genome-wide.
Single cell resolution
Go beyond population averages by measuring epigenomic profiles in single nuclei.
Flexible and scalable
Profile hundreds to tens of thousands of nuclei per chip.
Streamlined data analysis
Explore and visualize chromatin accessibility profiles with easy-to-use software.
One-day lab workflow
From sample to sequencing-ready library in one day.
Diverse sample compatibility
Demonstrated with cell lines, primary cells, and fresh and frozen tissue samples.
Explore what you can do
Define cell types and states
Identify master regulators
Discover cis-regulatory elements, such as promoters and enhancers
Characterize gene regulatory networks
Proven Results
Our End-to-End Solution
Chromium Single Cell ATAC Reagents
With our reagent kits, detect open chromatin regions using the included transposase, and generate ready-to-sequence NGS libraries.
Analysis and Visualization Software
Our analysis pipelines
Our visualization software
World-Class Technical and Customer Support
Our expert support team can be contacted by phone or email.
Workflow
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Prepare your sample
Start with a nuclei suspension isolated from cell culture, primary cells, or fresh or frozen tissue.
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Construct your 10x library
Construct a 10x barcoded single cell ATAC-seq library using our reagent kits and Chromium Controller. Nuclei are first transposed in bulk, and then encapsulated with a 10x barcoded Gel Bead using the Chromium Controller. Within each nanoliter-scale partition, transposed DNA fragments are labeled with 10x barcodes, where each barcode sequence represents a unique cell.
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Sequence
The resulting 10x Barcoded library is compatible with standard NGS short-read sequencing on Illumina sequencers, for massive transcriptional profiling of thousands of individual cells.
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Analyze Your Data
Our Cell Ranger ATAC analysis software generates open chromatin profiles for each cell, identifies clusters of cells with similar profiles and calls peaks, and can aggregate data from multiple samples.
Analysis pipelines output
Output includes QC information and files that can be easily used for further analysis in our Loupe visualization software, or third-party R, or Python tools.
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Visualize Your Data
Use our Loupe Browser visualization software to interactively explore your results, study expression patterns for genes of interest, determine cell types, and perform comparative analysis between clusters and samples.
Do I need to be a bioinformatician to use it?
Loupe is a point-and-click software that’s easy for anyone to download and use.
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Frequently Asked Questions
It enables profiling of the open chromatin landscape at single cell resolution.
Yes, using third party tools. For more information, watch our webinar.
A nuclei suspension is needed. It is possible to obtain high quality nuclei suspensions from fresh and cryopreserved cells, fresh tissue, and frozen tissue. This assay has been optimized for human and mouse samples, although other species may be possible.
Comparisons between bulk ATAC-seq and single cell ATAC-seq from cell lines indicates that single cell ATAC-seq recovers >=90% of peaks recovered by bulk ATAC-seq. Single cell ATAC-seq also provides the resolution to look at chromatin profiles at a cell-type specific level.
ATAC-seq captures all open chromatin regions, not just those bound by a specific factor. It is an unbiased approach to look for epigenetic changes in a sample. For proteins with a known sequence binding motif, the included software can identify those motifs that are enriched in open chromatin on a cell-by-cell basis.
