Xenium Tissue Optimization Protocol for PAXgene-Fixed Samples

An optimized workflow for applying Xenium automated in situ sequencing to PAXgene-fixed paraffin-embedded tissues. The dataset, authored by Kenny Roberts and last updated in May 2026, includes PNG files totaling 30.6 MB that likely contain results from systematic tests of permeabilisation conditions across multiple mouse and human tissues. It demonstrates that pepsin digestion can enhance RNA accessibility in PFPE samples to achieve spatial transcript detection comparable to FFPE and fresh frozen samples.

Use Cases

• Optimizing tissue-specific permeabilisation conditions for spatial transcriptomics based on the described Xenium Tissue Optimisation (XTO) protocol.
• Benchmarking RNA transcript detection rates in PAXgene-fixed tissues against FFPE and fresh frozen samples based on the described comparative results.
• Developing frameworks for applying in situ sequencing to archival sample collections based on the methodological workflow provided.

Strengths

• Dataset is openly licensed under CC-BY-4.0, permitting reuse with attribution.
• The description provides a specific methodological focus on optimizing Xenium for PAXgene-fixed tissues, a noted challenge in the field.
• Includes results from tests on multiple mouse and human tissue types, suggesting a multi-tissue validation scope.

Limitations

• The dataset consists of PNG image files; the underlying quantitative transcriptomic data is not directly provided.
• Row count and column-level documentation are unknown, limiting assessment of data scale and structure.
• Description metadata is limited; actual data quality requires manual inspection after download.

Provenance

Source

figshare

Collection Method

Systematic testing of permeabilisation conditions using a newly developed Xenium Tissue Optimisation protocol on mouse and human tissues.

Freshness

Last updated 2026-05-22 10:21:54; freshness should be verified.