Applying a structured spatial biology workflow in the lab involves careful attention to a sequence of technical stages. Success depends on the seamless connection between sample preparation, molecular capture, and data interpretation. We at STOmics have engineered our spatial omics solutions to bring coherence to this process. Our products provide the necessary components to operationalize a robust spatial biology workflow, guiding researchers from tissue section to spatial insight.

Commencing with Precise Tissue Handling

The initial stage of the spatial biology workflow is dedicated to sample preparation. This includes embedding, sectioning, and mounting fresh frozen or FFPE tissue onto our capture devices, such as the Stereo-seq Chips or Stereo-Chip Slides. Following this, tissue fixation and staining are performed using methods like ssDNA dye, DAPI, or H&E to visualize morphology. This imaging step, ideally performed with an upright microscope, creates a crucial anatomical reference. Executing this phase with consistency is vital, as it directly influences the quality of all subsequent data in the spatial biology workflow, forming the basis for truly integrated spatial omics solutions.

Executing Targeted Molecular Capture

The core of the method lies in capturing location-specific molecular information. The process differs slightly by sample type. For fresh frozen tissue, permeabilization allows mRNA to bind to spatially-barcoded probes on a Stereo-seq Chip T. For FFPE samples, permeabilization releases RNA to bind with random probes on a Stereo-seq Chip N for in situ cDNA synthesis. Critically, every cDNA molecule is tagged with a unique spatial barcode from its specific 500nm spot on the array. This precise tagging enables the high-resolution mapping that defines our spatial omics solutions. The resulting cDNA is then amplified into a sequencing library, compatible with platforms like DNBSEQ-T7RS or DNBSEQ-G400RS.

Completing the Cycle with Integrated Analysis

The final, indispensable phase transforms raw data into a spatial understanding. Sequencing files are processed through the Stereo-seq Analysis Workflow (SAW), a Linux-based pipeline that maps reads back to their original tissue coordinates. This computational step is followed by visualization and exploration in StereoMap, a cross-platform desktop application. Here, gene expression data is overlaid onto the tissue image, allowing for interactive analysis. This integration of SAW and StereoMap is a defining feature of our complete spatial omics solutions, providing the tools to extract biological meaning and effectively close the loop on the spatial biology workflow.

A reliable spatial biology workflow is more than a protocol; it is an integrated system where each step informs the next. From careful tissue preparation and barcoded molecular capture to dedicated bioinformatics, continuity is key. The products and spatial omics solutions offered by STOmics are specifically designed to ensure this continuity, providing researchers with a clear and effective framework to implement their studies.