Chromium GEM-X Technology

Single cell innovations & workflows built for your success

Chromium Technology
Single cell with confidence, at every workflow step
From sample prep to intuitive analysis, our workflows are designed for your success, no matter your experience. Count on our industry-leading technology and deep technical expertise to get high-quality, actionable insights for more sample types and applications.
Chromium Single Cell workflow step 1
Optimized sample prep for any single cell possibility

Profile fresh, frozen, and fixed samples—even FFPE—with sample prep methods optimized for your success. With 40+ Demonstrated Protocols across the breadth of our portfolio, your single cell studies can go further than ever before.

Chromium Technology tissue sample examples and a graphic of the Chromium X sample inputsChromium Technology tissue sample examples and a graphic of the Chromium X sample inputs
Access more sample types
  • Capture data from a wide range of species with our reverse transcription (RT)-based Universal assay
  • Expand the scope of your studies to include FFPE samples with our probe-based Flex assays
  • Easily isolate nuclei from frozen samples with kitted reagents and a unified workflow
Scale with flexible throughputs
  • Easily move from pilot studies to ambitious experiments with the ability to process 1–128 samples, and profile hundreds to millions of cells per run
  • Batch and run assays on your schedule with robust fixation protocols, even for whole blood samples
Increase efficiency with multiplex options
  • Use in-line multiplexing for fixed samples to profile up to 2.56M cells per run and enable sample batching
Read more below about our multiplexing technologies
Chromium Single Cell workflow step 2
Automated cell partitioning & barcoding
Ten years of experience and >$1.5B in R&D investment have come together in GEM-X's advanced microfluidic chip architecture and the innovative reagent delivery system of Chromium X series instruments.
Chromium Technology tissue sample examples and a graphic of the Chromium X sample inputs
GEMs: The core of Chromium Single Cell technology

Within Chromium X series instruments, cells move through the channels at a limiting dilution, generating 10,000+ nanometer-sized Gel Beads-in-emulsion (GEMs) in 4 minutes.

Each GEM is the site of a micro-reaction, in which Gel Beads are dissolved and target molecules from each cell are captured and barcoded, marking each target molecule's cell of origin.

The Chromium instrument advantage

Did you know? Chromium X series instruments automate the most critical steps in single cell assays: partitioning and barcoding.

These fast, efficient workflows reduce technical errors and batch effects common in labor-intensive, time-consuming manual workflows. Plus, the instruments combined with GEM-X advancements deliver industry-leading cell capture of up to 80% and superior reproducibility.

Chromium gel bead
Capture critical insights with higher-quality libraries
Optimized chemistry enables production of high-quality, sequencing-ready libraries with up to 95% usable reads.
One-day lab workflow

Go from sample to your sequencing-ready library in one day, with just 3 to 4 hours of hands-on time.

Barcoded fragments from GEMs are pooled for downstream reactions to create Illumina sequencer-compatible libraries:

  • MiSeq
  • NextSeq 500/550/2000
  • HiSeq 2500 (Rapid Run)
  • HiSeq 3000/4000
  • NovaSeq 6000
Detect more, sequence less
GEM-X chemistry ensures high-quality results, yielding libraries with high complexity and unmatched sensitivity. This means you can detect more genes at lower read depths plus experience improved detection of rare transcripts and cell types, including neutrophils, from complex samples from complex samples.
>40% higher sensitivity than other methods
Reduce reads by >60%, lowering your sequencing cost and maximizing your budget.
A graphic of strands of DNA
Graphic indicating step 3
Explore your data and make discoveries—no bioinformatics experience needed

Our intuitive and powerful software was developed to accelerate your access to experimental conclusions, whether you’re a seasoned pro or looking at your first dataset. Identify cell types and states, detect rare transcripts, perform multi-sample comparisons and more—all with free, user-friendly software.

Screenshots of 10x Genomics Chromium softare
  • Unlock downstream analysis with Cell Ranger, our easy-to-use pipelines that set the standard for scRNA-seq data processing
  • Get results quickly and run Cell Ranger at no cost per sample on 10x Genomics Cloud Analysis, our optimized cloud infrastructure
  • Visualize your processed data with the interactive Loupe Browser, quickly plotting differential expression of your favorite genes
  • Take advantage of continued innovations for new features like automated cell annotation
Versatile chemistries support a large range of inputs, applications & scales
Explore products
Reverse transcription (RT)-based assays
Captures the whole transcriptome alongside multiomic options (protein, CRISPR, BCR/TCR-seq, or open chromatin)
Graphic of reverse transcription
Why choose the RT-based Universal 3' or 5' assays?
  • Gather broad information (isoforms, single nucleotide polymorphisms, long non-coding RNAs, etc.) from diverse species
Probe-based assays
Uses probe sets against 18,000+ coding genes from human or mouse alongside protein readouts for fresh, frozen, and fixed samples
Graphic of reverse transcription
Why choose probe-based Flex assays?
  • Three-fold coverage of targets for high sensitivity and exceptional performance for FFPE and low-quality samples
  • Take advantage of the highest available throughput, 2.56M cells run on a single chip, for large-scale experiments
Streamlined multiplexing for flexible scaling & higher efficiency
In-line multiplexing and batching with Flex probe-based assays
Fix cell suspensions and hybridize prior to GEM generation, allowing pooling of up to 16 samples per channel
Graphic of reverse transcription
Why choose multiplexing with Flex?
  • Batch and multiplex to enable your largest studies, processing 1–128 samples and up to 2.56M cells per run
  • Bring convenience to your experimental workflow, streamlining ambitious projects and multi-site studies
GEM-X technology benefits
Higher performance powers higher success
Chart of GEM-X perhformace gains
Up to 2x
more genes
2x
more throughput
3x
faster run time
2x
lower multiplet rate
*Performance gains listed here reflect improvements of the GEM-X Universal 3' (2024) assay compared to the Next GEM Universal 3' assay (2018).
Icon of a sample in tube
More efficient GEM generation improves capture of fragile cells & does not increase cell stress
Icon of data visulization chart
Reduction of multiplet rate for enhanced data quality and robustness
Icon of a Chromium X
Higher throughput with up to 20,000 cells captured per channel at less than half the cost per cell
Icon of a Chromium X chip
Increased success rates with improvements in chip design that reduce clogging
Unlock the full spectrum of biology
Expand your Chromium Single Cell insights by combining by adding spatial context to the whole transcriptome or targeted genes.

Platform

Chromium Single Cell

Chromium Single Cell

See Chromium products
Visium Spatial

Visium Spatial

Xenium In Situ

Xenium In Situ

When to use

Comprehensive single cell data

Ideal for deep characterization of cell populations and states.

High-resolution spatial gene expression

Understand complex tissues, neighborhoods, and cell to cell interactions. Integration with other spatial-omics, histology, and morphology. 

Why to use

Unbiased single cell discovery

High per-gene sensitivity

Unbiased spatial discovery

Targeted spatial exploration

High per-gene sensitivity

Applications

Whole transcriptome gene expression

Protein

TCR, BCR

CRISPR

ATAC

Whole transcriptome gene expression

Targeted gene expression (up to 5,000 genes)

Resolution

Single cell

Transcripts assigned to 2-µm areas

Single cell

Data readout

NGS-based

NGS-based

Imaging-based

Sample compatibility

Single cell or nuclei suspensions from fresh, frozen, or FFPE samples

FFPE

Fresh frozen

Fixed frozen

Fresh frozen

FFPE