SureCell ATAC-Seq Library Prep Kit & Omnition Analysis Software

SureCell ATAC-Seq Library Prep Kit & Omnition Analysis Software

The SureCell 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.

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Overview

Download Omnition

The Bio-Rad Omnition Analysis Software Version 1.1.0 is a robust and efficient analysis pipeline for analyzing, visualizing, and reporting ddSEQ Single-Cell 3' RNA-Seq assay, SureCell ATAC-Seq assay, and ddSEQ-deployed combinatorial indexing ATAC protocols. The software is open-source and can be freely downloaded. Please see the user guide for further details.

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 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

  • SureCell ATAC-Seq Library Prep Kit

    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

    SureCell 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

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12004336

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

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Pkg of 1, complete reagents and consumables for the SureCell ATAC-Seq Library Prep Kit, includes ddSEQ M Cartridges (12009359), SureCell ATAC-Seq Reagent Box A (12009358) and SureCell ATAC-Seq Reagent Box B (12009357), for use with the ddSEQ Single-Cell Isolator
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12009358
Reagent set A for the SureCell ATAC-Seq Library Prep Kit, includes priming solution, droplet disruptor, encapsulation oil, and ATAC barcode mix, for use with the ddSEQ Single-Cell Isolator
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12009357
Reagent set B for the SureCell 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
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(Discontinued) ddSEQ M Cartridges
12009359

Pkg of 2, cartridges for use with the ddSEQ Single-Cell Isolator, the ddSEQ Single-Cell 3' RNA-seq Kit and the SureCell ATAC-Seq Library Prep Kit

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12009360
Pkg of 24, indexed primer pairs for use with the ddSEQ Single-Cell Isolator and the SureCell ATAC-Seq Library Prep Kit

Accessories

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cell counting feature
1450102

120–240 V, includes instrument, power supply, USB flash drive, 30 dual-chamber counting slides (60 counts), 1.5 ml trypan blue

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1851197

Modular thermal cycler platform, includes C1000 Touch Thermal Cycler chassis, 96–deep well reaction module, USB flash drive

Documents

Number Description Options
3354
Omnition Analysis Software Report Guide
3408
Omnition Analysis Software User Guide
7168
Droplet Digital™ Sequencing (ddSEQ™) Solution Publications List
10000106678
SureCell ATAC-Seq Library Preparation Kit User Guide
7191
Bio-Rad ATAC-Seq Analysis Toolkit Tutorial
7167
Single-Cell ATAC-Seq Flier
10000069430
ddSEQ Single-Cell Isolator Instruction Manual
ATAC-Seq_Poster
SureCell ATAC-Seq Library Prep Kit: A New Solution for Single-Cell ATAC-Seq using Bio-Rad's Droplet Digital Technology Poster