Single Cell 3’ Solution

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The Chromium Single Cell 3′ Solution

A Powerful Solution for Single Cell Discovery

The Chromium Single Cell 3′ Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to millions of cells. Affordable and with a simplified workflow, users can go from cell sample to sequencing library in less than one workday.

Our Solution Features

  • Complete workflow from cell suspension through sequencing-ready cDNA library in one day
  • Flexible throughput encapsulates 100 – 80,000+ cells in 10 minutes
  • Cell capture efficiency up to 65%
  • Compatible with Illumina® HiSeq®4000/2500/ NextSeq®/MiSeq® sequencers
  • More efficient than leading academic droplet systems
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The Chromium Controller

Compact, sleek, efficient.

The compact, sleek Chromium Controller has been designed to rapidly and efficiently automate the equivalent of 100,000s to 1,000,000s of pipetting steps for highly parallel sample partitioning and molecular barcoding. The Chromium Controller allows a user to run any of our Chromium Single Cell 3′, V(D)J, Genome and Exome Solutions. A dedicated Chromium Single Cell Controller is also available for users that exclusively run our Chromium Single Cell 3′ and V(D)J Solutions.

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Chromium Single Cell 3’ v2 Reagent Kits

All Chromium Controllers now support our new v2 single cell chemistry, with the following refinements:

  • Updated microfluidic chip to ensure robust priming, up to 65% cell capture efficiency and a reduced doublet rate
  • New inline barcoding scheme compatible with Illumina® HiSeq® 4000
  • Improved and shortened workflow based on enzymatic shearing
  • Higher number of transcripts detected per cell


  • Chromium Single Cell 3’ Library & Gel Bead Kit
    • 16 Reaction Kit
    • 4 Reaction Kit
  • Chromium Single Cell A Chip Kit
    • 6 Chips, 48 Reactions
    • 2 Chips, 16 Reactions
  • Chromium i7 Multiplex Kit
    • 96 Reactions
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Single cell RNA-seq data analysis and visualization

Paul Rivkin, PhD & Jeff Mellen
10x Genomics
November 28, 2017
Pleasanton, CA

Single cell sample preparation techniques and best practices

Jessica Terry, PhD & Jill Herschleb, PhD
10x Genomics
November 28, 2017
Pleasanton, CA

Harnessing the therapeutic potential of adoptively transferred cells

Aude Chapuis
University of Washington & Fred Hutchinson Cancer Research Center
June 22, 2017
Nature Webcast

Perturb-seq: Single-cell CRISPRi screens interrogate the Unfolded Protein Response

Britt Adamson
University of California, San Francisco
March 21, 2017
User Group Meeting – San Francisco, CA

Quantitative profiling of large and complex single cell populations

Grace Zheng
10x Genomics, Inc.
October 22, 2016
ASHG Annual Meeting – Vancouver, BC

Chromium single cell solutions

Tarjei Mikkelsen
10x Genomics, Inc.
October 21, 2016
ASHG Annual Meeting – Vancouver, BC

Defining the immune system at single cell resolution with Seurat

Rahul Satija
NYU Center for Genomics and Systems Biology
October 04, 2016
Nature Webcast

Massively-parallel single cell analysis with the Chromium System

Tarjei Mikkelsen
10x Genomics, Inc.
September 21, 2016
Pleasanton, CA

Analyzing immune cell communities on a massive scale with single-cell RNA-Seq

Cole Trapnell
University of Washington
April 21, 2016
Nature Webcast
*Pre-prints are available at BioRxiv.

Single cell transcriptomics for characterization of complex systems and biomarker detection

  • Single Cell Analyses
    Cold Spring Harbor Laboratory, New York
    November 8- November 11, 2017

High-throughput gene expression profiling of complex cell populations using the 10x Chromium Single Cell system

  • International Society for Computational Biology (ISMB) Annual Meeting
    Orlando, FL
    July 8 – 12, 2016

Deep profiling of thousands of cells from immune systems using scalable single gene expression

  • Gene Expression and Signaling in the Immune System
    Cold Spring Harbor, NY
    April 26 – 30, 2016

Single cell mRNA quantification from 1000s of cells in healthy and malignant tumor samples using a high-throughput droplet-based system

  • American Association for Cancer Research (AACR) Annual Meeting
    New Orleans, LA
    April 16 – 20, 2016

Order your Chromium Single Cell Controller, today.

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