Spatial Omics
Bring omics data into the spatial dimension and reconstruct molecular expression and tissue architecture in situ.
BGI Stereo-Seq (FF)
BGI Stereo-Seq FF spatial transcriptomics is an integrated solution achieving both 'nanoscale resolution' and 'centimeter-scale field of view' from tissue to data. Using Poly-T capture probes with spatial coordinates, it performs in-situ mRNA capture from fresh-frozen (FF) samples and reconstructs positions via spatial barcodes (Coordinate ID, CID). With excellent capture performance and a streamlined workflow, it captures high gene counts for easy CellBin analysis; combined with powerful tools, it explores spatiotemporal gene-expression patterns. Users may choose same-section nuclei or H&E staining. Unlike RNA-seq, which grinds tissue, Stereo-Seq FF preserves spatial structure while delivering near-single-cell transcriptomic information—ideal for tissue microregions, cellular neighborhoods, developmental trajectories, lesion boundaries, and microenvironment heterogeneity.
Principle Introduction
Stereo-Seq chips are pre-loaded with DNA nanoball probes carrying spatial coordinates. Fresh frozen sections adhere to the chip; released mRNA is captured in situ. Each probe carries a spatial barcode and molecular identifier. After RT, library prep, and sequencing, reads map back via spatial barcodes to reconstruct the spatial expression map. Compared with low-resolution spatial transcriptomics, Stereo-Seq has denser capture points for finer microregion boundaries and gradients; compared with in-situ panel technologies, it favors whole-transcriptome exploration.
Literature
Published in Cell, 'Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution' used BGI's Stereo-seq V2 FFPE whole-transcriptome technology (random-primer capture + thermo-decrosslinking) to achieve, for the first time at single-cell resolution, in-situ spatial analysis of total RNA (mRNA, lncRNA, pathogen RNA) on FFPE sections, with host–microbe co-analysis and BCR/TCR spatial tracking, overcoming poly(A) limits. TNBC FFPE stored 1 month–9 years (DV200 down to 18%), Mtb-infected mouse lung, and human TB lung were analyzed; 34 cell types in mouse brain FFPE, 1492 alternative splicing events and 6q24-25 amplification in TNBC, dynamic Mtb transcription and BCR affinity maturation in infection—establishing a new paradigm for FFPE single-cell spatial transcriptomics.
Experiment Flow
Sample evaluation
confirm tissue type, species, aim, section orientation and ROI.
Frozen embedding & sectioning
embed tissue in OCT and cut frozen sections for on-chip capture.
Tissue staining & imaging
stain and image the section to acquire morphology for annotation.
Permeabilization & capture
release RNA in situ and capture it on barcode probes on the chip.
RT & library prep
perform RT for cDNA synthesis, amplification and library construction.
Sequencing & bioinformatics
perform QC, alignment, clustering and spatial expression analysis.
Sample Requirements
embed within 30 min of dissection, or snap-freeze at -80°C.
tissue size should not exceed 0.9 × 0.9 × 2 cm (L×W×H); section/chip area should not exceed 80% of the spatiotemporal chip.
Deliverables
Expression matrix
spatial bin-level or near-cell-scale matrix, coordinates, detection info.
QC
sequencing quality, mapping rate, gene count, UMI count, tissue coverage, capture performance.
Basic analysis
dimensionality reduction/clustering, spatial clustering, marker genes, differential genes, enrichment.
Spatial visualization
morphology overlay, expression heatmap, regional maps, spatial differences.
Advanced analysis
cell-type mapping, spatial neighborhood, developmental/pathological comparison, single-cell integration.
Report
full project report, methods, key figures, interpretation, editable files.
FAQ
Complementary—Stereo‑Seq keeps space, scRNA‑seq gives deeper typing; joint analysis improves annotation.
Repeated freeze‑thaw, severe RNA degradation, high fat, ossification, fragile or easily detached sections—evaluate first.
