Human Skin FFPE Spatial Transcriptomics: Data Quality Recognized at the Highest Level by STOmics

Spatial transcriptomics is redefining how researchers interpret tissue organization and cellular interactions. However, when applied to FFPE samples—the most widely available resources in clinical and translational research—the technology encounters substantial limitations. RNA fragmentation, molecular crosslinking, and complex tissue structures often weaken spatial signals and reduce analytical reliability.

The Stereo-seq OMNI for FFPE workflow—STOmics’ latest total-RNA spatial transcriptomics solution—introduces significant improvements in sensitivity and signal stability, enabling high-quality profiling from degraded or archival FFPE samples.

As an early adopter working closely with STOmics, Omics Empower has fully implemented and optimized Stereo-seq OMNI for FFPE across our laboratories.

We are proud to share that our Stereo-seq OMNI for FFPE experimental data quality has received STOmics’ highest-level recognition under their official evaluation framework, highlighting our strong laboratory execution, spatial signal quality, and robust gene detection performance.

Today, we are releasing—for the first time—our experimental results from human skin FFPE tissue, a sample type that has long posed significant difficulties for spatial transcriptomics platforms.

A Demanding Benchmark: Why Human Skin FFPE Matters

Human skin FFPE tissue has long been considered one of the most challenging materials for transcriptomic analysis. Keratinization, stratified epidermal layers, and severe RNA degradation limit transcript accessibility and spatial resolution. These properties make skin FFPE an important stress test for any spatial technology aiming to support clinically relevant applications.

In September, Omics Empower conducted internal testing using a 1 cm × 1 cm Stereo-seq OMNI for FFPE chip with a sequencing depth of 2.36 G Total reads. This experiment provides a meaningful benchmark of the workflow’s performance in a highly degraded, structurally complex tissue.

First Public Release of Omics Empower’s Human Skin FFPE Stereo-seq Data

Despite the intrinsic challenges of skin FFPE, the workflow achieved strong transcript recovery and spatial clarity. At the bin level, the dataset reached an average of 1,625 MIDs and 938 detected genes, ultimately capturing more than 36,000 genes across the entire tissue section. These values illustrate the workflow’s capacity to extract biologically informative signals from deeply fragmented RNA.

At the finer single-cell level, STOmics’ CellBin segmentation further resolved the tissue into distinct spatial compartments. Average values of 510 MIDs and 347 detected genes per cell enabled a clear delineation of the stratum corneum, epidermis, and dermis. The resulting spatial map captures both large-scale tissue organization and subtle transcriptional differences across layers—observations that are rarely achievable with FFPE skin samples.

Figure 1:  Human skin FFPE spatial data (Stereo-seq OMNI, CellBin) generated by Omics Empower

Recognition From STOmics

STOmics’ assessment of our Stereo-seq OMNI for FFPE data considers multiple performance indicators, including spatial signal uniformity, gene detection capacity, microstructural resolution, and workflow reproducibility.

Based on these criteria, Omics Empower’s dataset was recognized at STOmics’ highest performance level, reflecting our technical accuracy across sample handling, chip processing, library preparation, and sequencing.

This recognition confirms Omics Empower’s ability to produce reliable, high-resolution spatial transcriptomic data from difficult FFPE specimens—a critical requirement for translational and clinical research applications.

Need Stereo-seq Spatial Transcriptomics Service?

If you are exploring Stereo-seq for your research, our team is ready to support you.

We offer an end-to-end Stereo-seq workflow—from sample preparation and chip selection to library construction, sequencing, and data analysis—so you can focus on the scientific questions. Our teams in Asia, Europe, and North America provide coordinated project support and reliable turnaround times for researchers worldwide.

Omics Empower combines extensive experience with FFPE and complex tissues, optimized wet-lab protocols, and high-resolution bioinformatics to ensure robust, publication-ready spatial transcriptomics data for projects of any scale.