Chromium GEM-X Technology

Single cell innovations & workflows built for your success

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.

1. Sample Prep

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.

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 1–3,072 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

Reduce reagent volumes and costs with easy on-chip multiplexing for Universal 3' and 5' assays
Use plate-based multiplexing for fixed samples to profile up to 8M cells per run and enable sample batching

2. Cell Partitioning & Library Prep

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.

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.

Capture critical insights with higher-quality librariesOptimized chemistry enables production of high-quality, sequencing-ready libraries with up to 95% usable reads.

One-day lab workflowGo 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 lessGEM-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.

Higher sensitivity maximizes your budgetReduce reads by >60%, lowering your sequencing cost.

3. Analyze

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.

Explore analysis software

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 pipelines 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

Probe-based assays

Uses probe sets against 18,000+ coding genes from human or mouse alongside protein readouts for fresh, frozen, and fixed samples

Why choose probe-based Flex assays?

Three-fold coverage of targets for high sensitivity and exceptional performance for FFPE and low-quality samples
Run large-scale studies (up to 384 samples a week) with convenient, plate-based multiplexing

Reverse transcription (RT)-based assays

Captures the whole transcriptome alongside multiomic options (protein, CRISPR, BCR/TCR-seq, or open chromatin)

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
Bring easy multiplexing to samples that can't be tagged (e.g., non-human/mouse, or nuclei) or samples that are limited

Streamlined multiplexing for flexible scaling & higher efficiency

Plate-based multiplexing and flexible batching with Flex

Why choose multiplexing with Flex?

Increase scale dramatically with convenient 96-well multiplexing and automation compatibility

Batch and multiplex to enable your largest studies, processing up to 384 samples or up to 100M cells per week
Scale at your pace by running partial plates, using only the reagents you need, when you need them

On-chip multiplexing for Universal 3' & 5' assays

Why choose on-chip multiplexing for Universal assays?

Co-partition cells from four samples, collect all GEMs in the same recovery well, and demultiplex samples computationally after sequencing

Process 1–8 samples and up to 40K cells/chip , with on-chip multiplexing for for any study, even at small scale
Add multiplexing to your workflow easily without the need to tag samples upstream of chip loading

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.See how researchers used Chromium, Visium, and Xenium to study human lung development

Platform	Chromium Single Cell See Chromium products	Visium Spatial Learn about Visium HD	Xenium In Situ Learn about Xenium
When to use	Comprehensive single cell dataIdeal for deep characterization of cell populations and states.	High-resolution spatial gene expressionUnderstand 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