StrataMap - Illumina
StrataMap (Illumina) is a sequencing-based spatial transcriptomics assay at 1 um resolution with very high sensitivity, capturing the whole transcriptome directly from the tissue section.
Specification
| Vendor | Illumina |
|---|---|
| Modality | sequencing-based spatial transcriptomics |
| Tissue | fresh frozen only |
| Capture area | 7.5 cm2 |
| Dimensions | 17 x 15 mm, 50 x 15 mm |
| Resolution | 1 um |
| Species | any eukaryotic |
| Billing | slide |
Accreditations & experience
The Spatial Technologies Unit has been an early adopter of StrataMap since December 2025, with service provision following validation and SOP completion in April 2026. Since then, the unit has performed numerous studies spanning human and animal-model samples.
Whole-transcriptome capture
StrataMap captures the whole transcriptome directly from the tissue section; the unit runs all available atlases.
- Whole Transcriptome: genome-wide RNA capture, the primary readout.
- RNA plex: whole transcriptome (unbiased, panel-free).
Additional capabilities
The workflow incorporates H&E staining and brightfield imaging of the section before capture, producing a co-registered tissue-morphology reference for each sample.
- Sequencing data are processed with the DRAGEN StrataMap Spatial pipeline into spatially resolved gene-expression matrices.
- Spatial data are visualised and analysed in Illumina Connected Multiomics, including cell segmentation, clustering, and cell-type identification.
What you receive
- FASTQ files and raw count matrices
- DRAGEN StrataMap Spatial pipeline outputs: spatially resolved gene-expression matrices
- co-registered H&E / tissue-morphology image
- post-processing QC metrics; MD5 checksums at transfer
Access and priority
Internal clients (BIDMC, DF/HCC), external academic and non-profit clients, and industry clients all have equal priority. Projects begin upon sample receipt.