Custom Probe-Based Spatial Transcriptomics Enables Microbiome Detection in FFPE Colorectal Cancer Tissue

ABSTRACT: We describe a custom probe design pipeline targeting the variable regions of bacterial 16S rRNA, compatible with the probe-based chemistry of the 10X Genomics Visium CytAssist platform, enabling spatially resolved bacterial profiling in FFPE tissue. Applied to a cohort of six FFPE colorectal cancer tumor and normal adjacent tissue specimens, we demonstrate the feasibility of a probe-based spatial metatranscriptomics for simultanous profiling of host gene expression and the intratumoral bacterial communities.

ORGANISM(S): Homo sapiens

PROVIDER: GSE334323 | GEO | 2026/06/08

REPOSITORIES: GEO