Archives of human tissue, vital for both research and diagnostics, are most commonly preserved as FFPE blocks. These samples are invaluable but present a well-known challenge for advanced molecular analysis due to RNA degradation caused by the fixation process. An FFPE transcriptomics solution is specifically designed to overcome this barrier, enabling researchers to extract and analyze genome-wide gene expression data from these precious, archived tissues. At STOmics, we have developed our own approach to this challenge. Our offering in this area, the STOmics OMNI platform, provides a dedicated spatial workflow to unlock the rich biological information stored in FFPE samples.

The Specific Challenge of FFPE Samples

The value of FFPE samples is immense, encompassing decades of clinical histories with associated patient outcomes. However, the very process that preserves tissue morphology—formalin fixation and paraffin embedding—cross-links and fragments RNA molecules. This makes traditional transcriptomic methods, which require high-quality RNA, difficult or impossible to use effectively. A capable FFPE transcriptomics solution must be engineered to work with this damaged, short-fragment RNA. It needs specialized chemistry to reverse cross-links, capture fragmented transcripts, and convert them into a library suitable for sequencing, all while preserving the spatial location of that RNA within the intact tissue section.

How a Spatial Solution for FFPE Functions

A spatial FFPE transcriptomics solution like our STOmics OMNI system operates through a coordinated series of steps. First, a thin section from the FFPE block is placed onto a specialized chip. The process then employs proprietary chemistry to reverse the formalin-induced cross-links and prepare the RNA for analysis. The key differentiator is what happens next: instead of homogenizing the tissue, the technology captures the RNA molecules directly in their original spatial positions on the chip. Each captured molecule is tagged with a spatial barcode that records its precise two-dimensional coordinates. After sequencing, these barcodes allow computational tools to reconstruct the complete transcriptome data back onto a high-resolution image of the original tissue architecture.

The Integrated Workflow from Sample to Insight

The practical utility of an FFPE transcriptomics solution lies in its integration. It is not just a reagent kit but a complete system. The STOmics OMNI platform exemplifies this as a coordinated workflow. It includes the optimized Stereo-seq chip for FFPE tissues, the specific reagent kits for library preparation, and the necessary instrumentation for imaging and processing. Crucially, it also encompasses the bioinformatics pipelines, like SAW and StereoMap, which are configured to handle the unique data characteristics from FFPE-derived sequences. This end-to-end design ensures that from a single, archived tissue section, researchers can generate a spatially resolved whole-transcriptome map, connecting histology with molecular function.

In essence, an FFPE transcriptomics solution is a specialized toolkit that makes the vast biobanks of archived tissues amenable to modern spatial biology inquiry. It solves the technical hurdle of degraded RNA to reveal the functional state of a tissue at the moment it was preserved. The STOmics OMNI platform provides our approach to this solution, integrating all necessary components into a defined spatial workflow. For STOmics, advancing these tailored solutions is central to our mission, empowering researchers to extract new insights from the world's most extensive collections of human tissue samples.