How to work with AtlasXomics
End-to-end spatial epigenomics,
built around your project
From sample qualification through sequencing and analysis — we handle as much or as little as you need. All services are built on the same DBiT-seq platform running in our facility.
Service options
Choose your level of support
Both options use the same core assay workflow. The difference is how much your team is involved in study design, data analysis, and project management.
Full project management
Best for first projects, pilots, clinical cohorts, and teams that want end-to-end support without dedicating internal bandwidth
- Study design consultation Included
- Sample qualification (AtlasVerify) Included
- Spatial profiling + library prep Included
- Shallow sequencing QC Included
- Deep sequencing Included
- Primary data processing Included
- Expert analysis + visualizations Included
- Interactive data portal access Included
- Dedicated project manager Included
Assay + data handoff
Best for teams with in-house bioinformatics who want to retain pipeline control using ArchR, Seurat, or SnapATAC2
- Planning call + design review Included
- Sample qualification (AtlasVerify) Optional
- Spatial profiling + library prep Included
- Shallow sequencing QC Included
- Deep sequencing Optional
- Primary data processing Optional
- Expert analysis + visualizations —
- Interactive data portal access Optional
- Dedicated project manager —
| What's included | White Glove | Standard |
|---|---|---|
| Study design session | ✓ | ✓ |
| AtlasVerify sample QC | ✓ | Optional |
| Spatial library prep | ✓ | ✓ |
| Shallow QC sequencing | ✓ | ✓ |
| Deep sequencing | ✓ | Optional |
| Primary bioinformatics | ✓ | Optional |
| Expert analysis + figures | ✓ | — |
| Interactive data portal | ✓ | Optional |
| Dedicated project manager | ✓ | — |
AtlasVerify
De-risk your samples before committing
A bulk in-situ qualification assay that runs on an adjacent section — generating an NGS library and a formal go/no-go recommendation before you invest in a full spatial experiment.
Know before you commit
FFPE tissue is highly variable in quality depending on fixation time, tissue age, and storage conditions. AtlasVerify gives you an objective, data-driven signal — not just a visual assessment — before committing a precious cohort to a full spatial assay.
For fresh-frozen samples, AtlasVerify is still recommended for first-time tissue types or samples with uncertain handling history.
Ship your slides
5–10 µm sections on standard 1×3" charged glass slides. An adjacent section is used for qualification — your primary sections remain intact.
In-situ bulk assay + shallow sequencing
We run an on-slide enzymatic reaction, build a bulk NGS library, and sequence to shallow depth to assess signal quality and library complexity.
Formal go/no-go recommendation
You receive a written report with QC metrics and a clear recommendation. Only proceed to full spatial assay when the data supports it.
Outcome: A written QC report with sequencing metrics and a clear go/no-go recommendation — so you make the call with data, not guesswork.
Data analysis
What you get from your data
All deliverables include pixel-level spatial maps. White Glove projects include expert analysis and publication-ready figures. Standard projects receive processed outputs compatible with standard single-cell tools.
Primary outputs
Aligned BAM files, peak calls, fragment files, and pixel-level feature matrices. Delivered in standard formats ready for downstream analysis in your tool of choice.
Spatial maps
Chromatin accessibility, histone mark enrichment, or methylation displayed spatially across the tissue section with H&E co-registration where available.
Expert analysis (White Glove)
Clustering, differential accessibility, motif enrichment, cell type deconvolution, and publication-ready figures tailored to your biological question.
Compatible analysis tools
Explore the analysis workflow
Analysis pipelines on GitHub
Open-source preprocessing and analysis scripts for Spatial ATAC-seq and CUT&Tag. Includes ArchR, SnapATAC2, and Snakemake-based workflows.
github.com/atlasxomics →Cloud analysis on LatchBio
Step-by-step tutorials for running AtlasXomics workflows on LatchBio — no local infrastructure required. From raw FASTQ to publication-ready figures.
View LatchBio tutorials →Sample requirements
What to send us
Not sure if your samples will work? Request an AtlasVerify evaluation before committing. Our team reviews all incoming samples before scheduling an assay run.
Fresh frozen (FF)
FFFFPE
FFPEFull workflow
From sample to insight
A typical White Glove project runs 6–10 weeks from sample receipt to final data delivery. Standard projects are faster depending on sequencing turnaround and whether deep sequencing is included.
01
Sample submission
Slides shipped per tissue type requirements
You do this02
AtlasVerify QC
Bulk in-situ qual + go/no-go report
Optional03
Spatial profiling
DBiT-seq barcoding + library prep
We handle04
Sequencing
Shallow QC checkpoint then deep sequencing
We handle05
Analysis + delivery
Expert report, portal, or raw outputs
We handle