US Based · Spatial Transcriptomics
Illumina StrataMap Spatial Transcriptomics Service
Unbiased whole-transcriptome mapping across a 15 x 50 mm capture area. Tissue embedding, sectioning, H&E imaging, slide placement, sequencing and full analysis, all in our SF Bay Area lab.
Assay
Illumina StrataMap
Capture area
15 mm x 50 mm
Species
Agnostic
Sequencing
NovaSeq X+ PE50
Read depth
5,000 reads/10×10 µm²
Turnaround
3 weeks + expedited
Price
$16,000/slide
Volume pricing available
Service Highlights
From tissue block to spatial map, all in one lab
Every stage runs in-house with defined QC criteria, from embedding and sectioning through sequencing and spatial analysis. Engage us for end-to-end service, or enter at the stage where you need support.
Tissue Prep
- OCT embedding
- TMA construction
- H&E staining and imaging
Slide Processing
- 1 µm capture array
- 15 mm x 50 mm capture area
- 3′ poly(A) hybridization capture
Sequencing
- Standard depth — 5k reads
- Deep coverage — 10k reads
- Illumina NovaSeq X+ PE50
Analysis
- Spatial expression maps
- Illumina DRAGEN analysis
- Advanced analysis options
Sample Requirements
Check your sample compatibility
Fresh or fresh-frozen tissue blocks only. Species agnostic, with a 15 mm x 50 mm capture area per slide. Send the block and we handle every upstream step. For tissue weight and size, read our FAQ.
| Sample type | SAMPLE REQUIREMENTS |
|---|---|
| Fresh tissue | Stored in Miltenyi MACS tissue storage solution and shipped chilled. We flash-freeze on receipt, then handle OCT embedding and cryosectioning. |
| Fresh frozen tissue | Shipped on dry ice. We perform OCT embedding, cryosectioning and placement. |
| OCT blocks | Pre-embedded OCT blocks shipped on dry ice. |
| TMA blocks | Existing TMAs accepted, or we can construct one so multiple cores share a single capture area. |
Alternative workflows
Need a different spatial resolution? Explore our other platforms below.
Need bulk RNA-Seq, single-cell, or multi-omic resolution?
Service Packages
Standard or deep coverage
Both packages run the same 15 mm x 50 mm capture area. Deep coverage doubles read depth for lower-abundance transcripts.
| Standard Service | Deep Coverage Service | |
|---|---|---|
| Solution | Standard Service — Illumina StrataMap | Deep Coverage Service — Illumina StrataMap |
| Species | Agnostic | Agnostic |
| Slide capture size | 15 mm x 50 mm | 15 mm x 50 mm |
| Data requirements | 5,000 reads / 10×10 µm² | 10,000 reads / 10×10 µm² |
| Sequencing — read length | NovaSeq X+ PE50 | NovaSeq X+ PE50 |
Every package includes
- 1 block QC (extraction and RIN)
- Sectioning
- 1 H&E stain
- Slide placement
- Library prep and QC
- Sequencing
- Data QC with FASTQ delivery
- Illumina DRAGEN spatial analysis package
Available as add-ons
- TMA construction
- Multiple block QC
- Pre-H&E staining
- Tissue morphology
- OCT embedding
- Permeabilization optimization
Technical excellence
Built for whole-transcriptome spatial capture
A 750 mm² capture area accommodates full tissue sections, or multiple sections and samples on a single slide. Cohorts, replicates and serial sections run in one experiment rather than one sample per slide, which removes the need to pre-select regions of interest and supports large-scale atlasing and spatial reconstruction workflows.
Tissue is permeabilized to release RNA while preserving spatial organization, then poly(A)-based capture hybridizes that RNA to spatially barcoded oligonucleotides across the surface. Spatially indexed cDNA links every transcript back to its tissue location, then is recovered and prepared as sequencing-ready libraries using standard Illumina workflows — no specialized spatial instrumentation required.
Service experience
Working with us
Every project is run by scientists, tracked in one portal, and processed entirely in our own lab.
PhD-Level Project Oversight
A PhD scientist owns your project from design through interpretation.
Dedicated Project Manager
One point of contact from quote through delivery.
Easy Ordering
Register samples, track status, and download results in one portal.
100% US-Based
Every stage runs in-house in Foster City, CA. No outsourcing.
Resources & insights
Technical resources
Brochure
Spatial Transcriptomics Brochure
Spatial transcriptomics with Signios Bio: where gene expression meets precision.
BLOG
Choosing the Best Spatial Service for Your Study
Visium HD vs. Xenium Prime vs. Illumina StrataMap — matching platform to study design.
BLOG
Integrating Single-Cell and Spatial Data
Building multimodal maps for translational research.
Frequently asked questions
Planning your spatial project
Samples & tissue prep
What sample types are compatible?
Which species are supported?
StrataMap is species agnostic. Because capture is unbiased and whole-transcriptome, there is no panel to design for your organism.
How large is the capture area?
15 mm x 50 mm per slide, the largest capture area of the spatial platforms we run. That footprint is what makes multi-specimen TMA layouts practical.
What sample prep services are supported?
OCT embedding, TMA construction, multiple block QC, pre-H&E staining and tissue morphology assessment are all available in house. They are quoted separately as add-ons to the core service package.
What is included in a package?
One block QC (extraction and RIN), sectioning, one H&E stain, slide placement, library prep, library QC, sequencing, and data QC with FASTQ delivery.
Data & delivery
How many transcripts are profiled?
The whole transcriptome, with no predefined panel. StrataMap captures genome-wide expression directly from tissue via 3′ poly(A) hybridization, so discovery is hypothesis-free rather than limited to selected genes. Transcript and gene counts per capture region depend on tissue type, RNA quality, and sequencing depth.
What read depth do I get?
What sequencing configuration is used?
How is my data delivered?
FASTQ files and a data QC report via secure FTP, available for 2 weeks with 60-day retention. Transfer to your own AWS, Globus or cloud storage is also available.
Ordering & logistics
How do I place an order?
Submit your inquiry below and our team will help create an account and walk you through sample submission.
How do I ship samples?
What is your typical turnaround time?
Standard turnaround is 3 to 4 weeks from the day your samples pass incoming QC to final data delivery. Expedited processing is available on every order — ask your project manager.
Is there a minimum number of samples?
There is no order minimum. Per-sample pricing improves with batch size, and a TMA layout can place several specimens on one capture area.
Get started with your project
Ready to uncover spatially resolved transcriptomic insights from your tissue samples? Contact our team for a technical consultation. We’ll guide you through sample requirements, tissue preparation, workflow planning, and sequencing considerations.
- Spatially resolved transcriptomic profiling
- Works with fresh, frozen, and archived tissue
- Sample and workflow guidance from our technical team
- Sequencing and data analysis support