Effective research outcomes with spatial transcriptomics hinge on meticulous preliminary work. For scientists utilizing the STOmics platform, proper sample preparation is the critical first phase that influences all subsequent data quality. This guide outlines key steps to prepare tissue sections for a Stereo-seq run, focusing on practices that help reveal spatial transcriptomics trait-associated cells.
Selecting and Preserving Tissue Specimens
The process begins at the biopsy stage. Choosing the correct tissue region of interest is paramount, especially when the research goal is to locate specific spatial transcriptomics trait-associated cells. Immediate and appropriate preservation, typically through flash-freezing in optimal cutting temperature compound or formalin fixation, is essential to maintain RNA integrity. This preserves the native spatial context of gene expression for the STOmics platform’s analysis.
Sectioning, Mounting, and Permeabilization
Frozen blocks are cryo-sectioned, or FFPE samples are sliced, onto specific capture areas. Sections must be thin, typically 5-10 µm, and flat to ensure uniform contact with the Stereo-seq chip’s surface. Proper mounting avoids folds or tears that compromise spatial data. A subsequent permeabilization step carefully lyses cells to release RNA molecules while preserving tissue architecture. This balance is crucial for capturing the full transcriptome profile from discrete cellular locations.
Quality Control and Staining
Before sequencing, rigorous quality checks are non-negotiable. Histological staining, such as H&E, is performed on a consecutive section or the same one after imaging. This provides a morphological reference map to correlate with the final spatial transcriptomics data. Assessing RNA quality (e.g., RIN number) from an adjacent tissue punch confirms sample viability. These controls directly impact the ability to identify subtle spatial transcriptomics trait-associated cells within the tissue landscape.
Adhering to a consistent and optimized sample protocol lays a reliable foundation for the high-resolution data generated by the STOmics Stereo-seq technology. Attention to detail in these initial stages empowers researchers to confidently progress to sequencing and computational analysis, maximizing the return from their spatial transcriptomics investigation with the STOmics platform.
