The Bio-Rad Omnition Analysis Software Version 1.0.0 (ATAC module) is a robust and efficient analysis pipeline for analyzing, visualizing, and reporting single-cell ATAC-Seq data produced with the SureCell ATAC-Seq assay and ddSEQ-deployed combinatorial indexing ATAC protocols. It is made open-source and available to download.
The SureCell ATAC-Seq Library Prep Kit and Omnition Analysis Software enable reproducible genome-wide profiling of the epigenomic landscape at the single-cell level with a high number of unique reads per cell so you can better understand the mechanisms that drive how genes are regulated.
Features and Benefits
- Greater than 65% and up to 95% cell capture efficiency
- Adjustable cell throughput range of as few as 400 or more
than 5,000 cells per sample
- Best sensitivity possible from the highest number of unique sequencing fragments that map to the nuclear genome, ATAC peaks, and transcription start sites
- A powerful and efficient informatics tool in a flexible pipeline
- Runs on the ddSEQ Single-Cell Isolator
- Works with nuclei or whole cells
How Single-Cell ATAC-Seq Works
The SureCell ATAC-Seq Library Prep Kit and Omnition Analysis Software by Bio-Rad enable reproducible genome-wide profiling of the epigenomic landscape at the single-cell level with a high number of unique reads per cell so you can better understand the mechanisms that drive how genes are regulated.
Applications and Uses
- Answer deep questions about regulation of gene expression through interrogation of promoters, enhancers, or other regulatory elements
- Characterize relationships between cis-regulatory elements and non-coding genetic variation
- Validate scRNA-Seq studies as an orthogonal approach
Dr. Jason Buenrostro Discusses Exciting ATAC-Seq Applications
Map open chromatin and understand the machinery behind gene regulation in exquisite detail at the single-cell level with ATAC-Seq.
SureCell ATAC-Seq Library Prep Kit
- ddSEQ M Cartridges
- SureCell ATAC-Seq Reagent Box A
- SureCell ATAC-Seq Reagent Box B
SureCell ATAC-Seq Index Kit
- 24 Indexes
- Dataset 1 — Mouse Brain (46,653 cells): Frozen whole brain tissue from two adult mice, purchased from BrainBits, and processed according to the Omni-ATAC Protocol to isolate nuclei.1
- Dataset 2 — Combinatorial profiling of resting and stimulated bone marrow (136,463 cells): Frozen human bone marrow mononuclear cells from AllCells, stimulated with and without LPS, and barcoded with 96 indexed Tn5 transposases prior to droplet encapsulation.2
- Dataset 3 — Isolated populations from peripheral blood (52,873 cells): Frozen human bone marrow CD34+ stem/progenitor cells, and isolated peripheral blood CD4+ T cells, CD8+ T cells, Monocytes, B cells, and NK cells, bought from AllCells and processed according to the Whole-Cell Protocol provided in the ATAC-Seq User Guide.3
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ddSEQ Single-Cell Isolator is a droplet-based single cell isolation system for single-cell chromatin accessibility studies. The system includes the isolator, test cartridges and the cartridge holder
Pkg of 1, 96-Well Plate Cooling Block for use with the ddSEQ™ Single-Cell Isolator
Pkg of 1, replacement cartridge holder for the ddSEQ Single-Cell Isolator
Pkg of 2, replacement test cartridges for use with the ddSEQ Single-Cell Isolator
Pkg of 25, clear well/clear shell semi-skirted plates, for use with QX600/QX200 Droplet Digital™ PCR Systems
Modular thermal cycler platform, includes C1000 Touch Thermal Cycler chassis, 96–deep well reaction module, USB flash drive