SERVICE OFFERINGS
Spatial and Single Cell Applications
Compare capabilities to find the right solution for your research
Compare the whole-transcriptome spatial services from 10x Genomics.
Visium HD assays
Single-cell–scale resolution
Probe-based chemistry
Supports human & mouse FFPE, fresh-frozen, and fixed-frozen tissue
Reverse-transcription–based chemistry
Species-agnostic fresh-frozen tissue compatibility
Multiomic readouts from the same section:
Gene expression
Protein co-detection (immunofluorescence)
Morphology (H&E)
Visium v1 and v2 assays
1-10 cell resolution
Probe-based chemistry (v2)
Human and mouse FFPE, fresh frozen, and fixed frozen tissue
Reverse transcription–based chemistry (v1)
Species agnostic, fresh frozen tissue
Multiomic readouts from the same section:
Gene expression
Protein co-detection (immunofluorescence)
Morphology (H&E)
Human immuno-oncology protein panel (v2)
Compare the Single Cell service offerings from 10x Genomics.
Chromium Single Cell
GEM-X Flex Gene Expression
Comprehensive whole-transcriptome gene expression with unmatched flexibility in sample prep and the freedom to fix, batch, and process samples on your own schedule.
Recommended for experiments that…
- Use archival or lower-quality samples
- Require flexible sample batching
- Will scale up and require the lowest cost per-cell
Chromium Single Cell
GEM-X Universal 3’ Gene Expression
This is a flexible 3′ gene expression platform with built-in multiomic analysis capabilities.
Recommended for experiments that…
- Require full-length transcript readouts, with or without simultaneous protein expression
- Only require gene expression, or may use ATAC in the future
- Have lower cell input requirements
Chromium Single Cell
GEM-X Universal 5’ Gene Expression
In‐depth immune diversity analysis uniting 5′ gene expression with advanced multiomic workflows.
Recommended for experiments that…
- Require full length transcript readouts, with or without simultaneous protein expression
- Require or may use CRISPR and TCR/BCR sequencing in the future
- Have lower cell input requirements
GEM-X Flex Gene Expression
Primary capability
Probe-based gene expression
Analyze gene expression using pre-designed probes with the option to add custom probes
Multiomic capabilities
Cell surface protein
Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions
CRISPR screening
Assess effects of CRISPR perturbations at single cell resolution with direct capture of cellular sgRNAs and changes in gene expression
Intracellular protein
Achieve detection of proteins throughout the entire cell, including nuclear, cytosolic, and secreted proteins
Compatible species
Human
Mouse
Additional species
Compatible sample types
Cell suspension
Nuclei suspension
Fresh tissue
Frozen tissue
FFPE tissue
PFA-fixed tissue
Flow-sorted cells
Fixed whole blood
Organoids
GEM-X Universal 3' Gene Expression
Primary capability
3' gene expression
Detect and quantify RNA molecules near the 3' end of genes
Multiomic capabilities
Cell surface protein
Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions
Compatible species
Human
Mouse
Rat
Non-human primate
Marine
Plant
Insect
And more
Compatible sample types
Cell suspension
Nuclei suspension
Fresh tissue
Frozen tissue
Fixed human PBMCs
Flow-sorted cells
Organoids
GEM-X Universal 5' Gene Expression
Primary capability
5' gene expression
Detect and quantify RNA molecules near the 5' end of genes
Multiomic capabilities
Cell surface protein
Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions
CRISPR screening
Assess effects of CRISPR perturbations at single cell resolution with direct capture of cellular sgRNAs and changes in gene expression
TCR/BCR sequencing
Understand clonal expansion and diversity by capturing full-length, paired B-cell and T-cell receptors
Antigen specificity
Interrogate the binding of antigens to immune cell receptors to fully characterize the adaptive immune response.
Compatible species
Human
Mouse
Rat
Non-human primate
And more
Compatible sample types
Cell suspension
Nuclei suspension
Fresh tissue
Frozen tissue
(gene expression only)
Fixed human PBMCs
Flow-sorted cells
Organoids
Primary capability
Probe-based gene expression
Analyze gene expression using pre-designed probes with the option to add custom probes
3' gene expression
Detect and quantify RNA molecules near the 3' end of genes
5' gene expression
Detect and quantify RNA molecules near the 5' end of genes
Multiomic capabilities
Cell surface protein
Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions
Cell surface protein
Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions
Cell surface protein
Identify surface protein markers to categorize cell types, pinpoint biomarkers, and explore cell signaling and interactions
CRISPR screening
Assess effects of CRISPR perturbations at single cell resolution with direct capture of cellular sgRNAs and changes in gene expression
CRISPR screening
Assess effects of CRISPR perturbations at single cell resolution with direct capture of cellular sgRNAs and changes in gene expression
Intracellular protein
Achieve detection of proteins throughout the entire cell, including nuclear, cytosolic, and secreted proteins
TCR/BCR sequencing
Understand clonal expansion and diversity by capturing full-length, paired B-cell and T-cell receptors
Antigen specificity
Interrogate the binding of antigens to immune cell receptors to fully characterize the adaptive immune response.
Compatible species
Human
Mouse
Additional species
Human
Mouse
Rat
Non-human primate
Marine
Plant
Insect
And more
Human
Mouse
Rat
Non-human primate
And more
Compatible sample types
Cell suspension
Nuclei suspension
Fresh tissue
Frozen tissue
FFPE tissue
PFA-fixed tissue
Flow-sorted cells
Fixed whole blood
Organoids
Cell suspension
Nuclei suspension
Fresh tissue
Frozen tissue
Fixed human PBMCs
Flow-sorted cells
Organoids
Cell suspension
Nuclei suspension
Fresh tissue
Frozen tissue
(gene expression only)
Fixed human PBMCs
Flow-sorted cells
Organoids
GEM-X Flex Gene Expression
GEM-X Universal 3' Gene Expression
GEM-X Universal 5' Gene Expression
Additional Spatial & Single Cell Services
3D Genomics is happy to engage with your projects using additional spatial and single cell assays. Please inquire about the use of Curio, Stomics, Parse, BD or Scale technologies.
Additional CRO Services
Confocal Imaging
- Biomarker imaging for spatial multiomics
- Proteomic vaildation of spatially distinct cell states
FACS isolation of Cell Subsets
- Bulk cell enrichment by magnetic bead isolation
- Antibody specific cell type isolation by FACS
In-Depth Bioinformatics
- Detailed informatics and data visualization
- Data integration for multiomics
- Custom analysis workflows
High Content Imaging
- High Content Analysis/Screening
- 2D, co-culture, 3D imaging
- Drug response HCS
- Cell Painting assay
Custom Assay Development
- Compound validation assays
- Complex dosing schemes
- Full gamut of phenotypic and molecular readouts
How to Work With Us
Sample Collection
Send Tissue or Cells
Sample Prep, Library Prep & Sequencing
Histology, Single Cell Isolation, Spatial and Single Cell Library Preparation
Data Analysis
QC, Sequencing & Primary Analysis Files prepared and sent.
Ready to move your spatial and single cell research forward?
Partner with 3D Genomics for high-resolution spatial and single-cell transcriptomics services that move your research forward.
