ddSEQ Single-Cell ATAC-Seq Library Prep Kit & Omnition Analysis Software
The ddSEQ Single-Cell ATAC-Seq Library Prep Kit is a single-cell ATAC-Seq assay for genome-wide open chromatin interrogation. Leveraging Bio-Rad’s ddSEQ droplet technology, this assay is able to capture and profile hundreds to thousands of single cells with high sensitivity and recovery. The ddSEQ single-cell ATAC-Seq assay along with the Omnition Analysis Software, together, provides a robust and cost-efficient solution to better understand the regulatory landscape of individual cells.
Overview
Download Omnition
Omnition Analysis Software Version 1.1.0 is a robust, efficient open-source analysis pipeline for analyzing, visualizing, and reporting data from the ddSEQ Single-Cell 3' RNA-Seq assay, the ddSEQ Single-Cell ATAC-Seq assay, and ddSEQ-deployed combinatorial indexing ATAC protocols.
The ddSEQ Single-Cell ATAC-Seq Library Prep Kit and Omnition Analysis Software enable reproducible genome-wide profiling of the epigenomic landscape at the single-cell level with high sensitivity and resolution.
Features and Benefits
- Greater than 65% 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
Applications and Uses
- Understand regulation of gene expression through interrogating chromatin accessibility and characterizing transcription factor binding
- Identify unique subpopulations of cell types based on their open chromatin profiles
- Validate single-cell RNA-seq results
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.
Included Components
ddSEQ Single-Cell ATAC-Seq Library Prep Kit
ddSEQ M Cartridges
ddSEQ Single-Cell ATAC-Seq Reagent Box A
ddSEQ Single-Cell ATAC-Seq Reagent Box B
ddSEQ Single-Cell ATAC-Seq Index Kit
24 Indexes
Data Sets
- 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
*Datasets are from SubSeries that are part of the SuperSeries cited below.
SuperSeries: Lareau CA, Duarte FM, Chew JG, Kartha VK et al. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nat Biotechnol 2019 Aug;37(8):916-924.
Example Omnition Reports
- Single-cell ATAC-Seq data analysis report
- Single-cell combinatorial indexing ATAC-Seq data analysis report
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ddSEQ Single-Cell Isolator is a droplet-based single cell isolation system for single-cell gene expression and gene regulation studies. The system includes the isolator, test cartridges and the cartridge holder
Pkg of 1, complete reagents and consumables for the ddSEQ Single-Cell ATAC-Seq Library Prep Kit, includes ddSEQ M Cartridges (12009359), ddSEQ Single-Cell ATAC-Seq Reagent Box A (12009358) and ddSEQ Single-Cell ATAC-Seq Reagent Box B (12009357), for use with the ddSEQ Single-Cell Isolator
Reagent set A for the ddSEQ Single-Cell ATAC-Seq Library Prep Kit, includes priming solution, droplet disruptor, encapsulation oil, and ATAC barcode mix, for use with the ddSEQ Single-Cell Isolator
Reagent set B for the ddSEQ Single-Cell ATAC-Seq Library Prep Kit, includes ATAC PCR supermix, ATAC enhancer enzyme, ATAC primer mix, ATAC tagmentation buffer, ATAC tagmentation enzyme, ATAC enzyme buffer, ATAC enzyme, and ATAC sequencing primer, for use with the ddSEQ Single-Cell Isolator
Pkg of 2, cartridges for use with the ddSEQ Single-Cell Isolator, the ddSEQ Single-Cell 3' RNA-seq Kit and the ddSEQ Single-Cell ATAC-Seq Library Prep Kit
Pkg of 24, indexed primer pairs for use with the ddSEQ Single-Cell Isolator and the ddSEQ Single-Cell ATAC-Seq Library Prep Kit
Accessories
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
120–240 V, includes instrument, power supply, USB flash drive, 30 dual-chamber counting slides (60 counts), 1.5 ml trypan blue
Modular thermal cycler platform, includes C1000 Touch Thermal Cycler chassis, 96–deep well reaction module, USB flash drive