FlowGel Spatial Barcoding Kits
Bring spatial epigenomics
into your own lab
The FlowGel platform integrates directly into standard pathology and single-cell workflows — no custom instruments, no proprietary hardware. One protocol across all modalities: ATAC, CUT&Tag, methylation, and co-profiling.
Assay kits
Choose your assay
All kits share a common core protocol. Learn one modality and you can run them all with minimal additional training.
Spatial ATAC-seq
Map open chromatin across intact tissue to identify regulatory programs and cell-type-specific accessibility at spatial resolution.
What you get
- Pixel-level chromatin accessibility maps
- Peak calls + fragment files
- Cell-type deconvolution-ready outputs
- Compatible with ArchR, SnapATAC2
Spatial CUT&Tag
Profile histone modifications (H3K27me3, H3K4me3, and others) with spatial context across intact tissue sections.
What you get
- Spatial histone mark enrichment maps
- Peak calls per spatial pixel
- H&E co-registration ready
- Compatible with ArchR, Seurat
TAPS+ / Co-profiling
Simultaneously profile chromatin accessibility and DNA methylation, or combine ATAC with spatial gene expression in a single assay.
What you get
- Dual-modality spatial maps
- Accessibility + methylation co-registered
- Single library prep workflow
- Compatible with custom pipelines
Not sure which assay is right for your project?
Compare assays side by side — sample compatibility, resolution, modality, and best use cases.
Platform & hardware
What you need to get started
The FlowGel platform is a fluidics-free evolution of DBiT-seq. It's designed to integrate into workflows you already have — no custom instruments, just one accessory.
AtlasXpress accessory
The single required accessory — ensures precise placement of the microfluidic chip onto your tissue section on a standard 1×3" charged glass slide.
RequiredBasic epifluorescence microscope
Standard fluorescence microscope for tissue imaging and spatial alignment. No confocal or specialized optics required.
Standard lab equipmentCommon molecular biology tools
Standard pipettes, thermal cycler, centrifuge, and reagents already in any single-cell or molecular biology lab.
Standard lab equipmentNGS sequencer
Libraries are compatible with standard Illumina sequencing workflows — the same setup you use for single-cell ATAC-seq or RNA-seq.
Standard lab equipment10 × 10 µm resolution
48,400 spatial spots per chip on a 5.5 × 5.5 mm capture area. Fits directly on standard 1×3" charged glass slides used in pathology workflows.
What's included
Everything in the kit
Each Spatial Reagent Kit includes all reagents and chips needed to generate a spatial epigenomics library, ready for standard NGS sequencing.
Spatial Reagent Kit
Core kit — included with every assay
- Microfluidic barcoding chips (A + B arrays)
- In-situ enzymatic reagents (assay-specific)
- Ligation and library prep reagents
- Indexed sequencing adapters
- Quality control oligos
- Buffers and wash solutions
- Step-by-step protocol guide
AtlasXpress Accessory
One-time purchase — works with all kits
- Chip placement guide + alignment tool
- Compatible with standard 1×3" slides
- Works across all FlowGel assay types
- Quick-start setup guide included
- Replacement parts available separately
Already have AtlasXpress? You only need to reorder reagent kits for subsequent runs — no need to repurchase the accessory.
Workflow
From slide to sequencing-ready library
The FlowGel workflow follows the same steps across all modalities. Experienced single-cell labs typically complete library prep in 2 days.
01
Tissue prep
Section tissue onto standard 1×3" charged slides. FF at 7–10 µm, FFPE at 5 µm.
02
Permeabilization
On-slide enzymatic permeabilization optimized for tissue type and assay.
03
Spatial barcoding
AtlasXpress places microfluidic chips. Two orthogonal flows deliver A×B barcodes.
04
Library prep
Extract barcoded molecules, amplify, and build indexed sequencing libraries.
05
Sequencing
Load onto standard Illumina instrument using familiar single-cell workflows.
Sample requirements
Preparing your tissue
FlowGel kits are compatible with both fresh-frozen and FFPE tissue. If you're uncertain about sample quality — especially for FFPE — consider running AtlasVerify before your first kit run.
Fresh frozen (FF)
FFFFPE
FFPEWorking with FFPE?
FFPE quality varies significantly by fixation time and storage. Run AtlasVerify on an adjacent section before committing your cohort to a full kit run.
Resources
Everything you need to run our kits
Protocols, videos, and analysis tools — all in one place.
White paper
Oncology case study — spatial ATAC-seq in tumor tissue
Read white paper →
Video
High-level overview of AtlasXomics kits
Watch video →
Video
Watch our scientists run the kits in the lab
Watch video →
Protocol
Step-by-step tissue preparation and library prep protocol
Read protocol →
Tutorial
Run analysis locally or in the cloud with LatchBio
View tutorial →
GitHub
Open-source analysis pipelines — ArchR, SnapATAC2, Snakemake
View on GitHub →
FAQ
Common questions
Have a question not covered here? Talk to a scientist.
Do I need to purchase new kits for each assay type?
Yes — each assay type (ATAC, CUT&Tag, TAPS+) uses a different Spatial Reagent Kit with assay-specific reagents. However, the AtlasXpress accessory is a one-time purchase and works across all kit types.
How long does the workflow take from slide to sequencing-ready library?
Most experienced single-cell labs complete the full workflow in approximately 2 days. Day 1 covers tissue prep, permeabilization, and barcoding. Day 2 covers ligation, library amplification, and QC.
Can I use my existing single-cell ATAC-seq analysis pipeline?
Yes, with some modifications. Fragment files output from AtlasXomics kits are compatible with ArchR, SnapATAC2, and Seurat. Spatial context requires incorporating our coordinate files — tutorials and scripts are available on our GitHub and via LatchBio.
Is FFPE tissue compatible with all kit types?
FFPE is currently supported for Spatial ATAC-seq and TAPS+. CUT&Tag on FFPE is under active development. We recommend running AtlasVerify on your FFPE samples before committing to a full kit run, as FFPE quality varies significantly.
What sequencing depth is recommended?
We typically recommend 25,000–50,000 reads per spot for ATAC-seq. CUT&Tag may require higher depth depending on the histone mark. Detailed sequencing recommendations are included in each kit protocol.
What if my samples don't perform well?
Contact your AtlasXomics support scientist. We offer troubleshooting support for all kit customers. For future runs, consider using AtlasVerify to qualify samples before running the full assay.