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 <7 hours
  • Flexible throughput encapsulates 700-70,000 cells in 10 minutes
  • Cell capture efficiency >65% for rare cell types in heterogeneous populations
  • 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.

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Chromium Single Cell 3’ v2 Library
& Gel Bead Kit

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

  • Updated microfluidic chip to ensure robust priming, >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’ Gel-Bead Kit
  • Chromium Single Cell 3’ Chip Library Kit
  • Chromium Single Cell 3’ Chip Kit
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Single Cell Datasets

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Chromium Single Cell 3’ Solution

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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
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Massively parallel digital transcriptional profiling of single cells

Zheng GX et al. Nat Commun. 2017 Jan 16;8:14049. doi: 10.1038/ncomms14049. PMID: 28091601.

A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response

Adamson B et al. Cell. 2016 Dec 15;167(7):1867–1882. doi: 10.1016/j.cell.2016.11.048. PMID: 27984733.

Perturb-Seq: Dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens

Dixit A et al. Cell. 2016 Dec 15;167(7):1853–1866. doi: 10.1016/j.cell.2016.11.038. PMID: 27984732.

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

Wang B et al. 2016 Jun 9; Pre-print*.
*Pre-prints are available at BioRxiv.
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Single cell mRNA quantification from 1000s of cells in intestinal epithelial cells and bone marrow mononuclear cells using a high-throughput droplet-based system

  • Wellcome Trust Single Cell Genomics Conference
    Cambridge, UK
    September 14 – 16, 2016