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.

The 10X Single Cell 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

page-single-cell-controller-pictureThe 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′, Genome and Exome Solutions. A dedicated Chromium Single Cell Controller is also available for users that exclusively run our Chromium Single Cell 3′ Solution.


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
  • Chromium Single Cell 3’ Chip Kit
  • Chromium i7 Multiplex Kit


Cell Ranger™ 1.3 – New Features

  • Improved demultiplexing workflow
  • Data aggregation
  • Large-scale analysis of up to 1 million cells

Cell Ranger™: Pipelines

A set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.

Loupe™ Cell Browser

An interactive visualization tool for anyone to gain insight from the Chromium Single Cell 3′ Solution. Easily perform single-cell data analysis to identify populations, isolate significant genes, measure expression levels, and export your findings.


Scientific Seminars

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


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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