StereoMap

The Stereo-seq OMNI for FFPE Solution advances spatial biology by providing a transcriptomics solution specifically designed for formalin-fixed, paraffin-embedded (FFPE) tissues. It offers true single-cell resolution and comprehensive RNA profiling, addressing the challenges posed by RNA degradation and protein cross-linking typical in FFPE processing. This is achieved through an innovative Random Probe hybridization approach that efficiently captures total RNA, including coding, non-coding, and microbial RNAs.

Capable of working with samples having RNA integrity levels as low as DV200 ≥ 30%, this solution opens up vast archives of clinically annotated tissues for spatial transcriptomics analysis. It is applicable to diverse tissues from various species, facilitating the exploration of relationships between gene expression, cellular morphology, and microenvironmental factors.

Key Features

• Total RNA Capture: Utilizes an innovative Random Probe design for efficient capture of coding and non-coding RNAs.
• Compatibility with Low-Quality Tissues: Works with archived clinical specimens with DV200 > 30%.
• True Single-Cell Resolution: Allows visualization of gene expression patterns at sub-micron resolution with exceptional clarity.

The Stereo-seq Analysis Workflow (SAW) is a software suite that maps sequenced reads to their spatial location on a tissue section, quantifies spatial feature expression, and visually presents the spatial expression distribution. StereoMap, a desktop application, provides essential analysis functionality for interactive exploration of Stereo-seq data.

This solution integrates seamlessly with standard histopathology workflows, enabling correlative analysis of gene expression patterns with morphological features in the same tissue section. It is transformative for studying tumor heterogeneity, immune cell interactions, and developmental processes in archived samples, bridging historical clinical data with spatial insights.

In disease progression studies, the solution has identified distinct transcriptional disruptions in Alzheimer’s disease patients, highlighting significant reductions in specific neuronal interactions linked to cognitive decline. Its nanoscale resolution and whole-transcriptome coverage allow precise pathological mapping, revealing neuronal loss and signaling reductions.

In tumor microenvironment studies, the solution has identified spatially distinct transcriptional subclusters and novel biomarkers, offering insights into the molecular basis of spatial cell heterogeneity and crosstalk within the tumor microenvironment.