10x Xenium

Overview

10x Genomics Xenium is an in situ single-cell spatial gene-expression platform. It uses combinatorial fluorescence in situ hybridization (FISH) chemistry to simultaneously detect hundreds of RNA targets at single-molecule resolution within intact tissue sections, preserving spatial context while delivering single-cell sensitivity.

Used by

• PMID:41941260 — Xenium single-cell spatial profiling was applied at KIDSROBIN to baseline and post-131I-MIBG second-look neuroblastoma samples; identified differentially depleted and enriched cell populations following radiopharmaceutical therapy PMID:41941260.
• PMID:39975212 — 10X Xenium used for single-cell spatial profiling of FFPE skin sections (two adjacent sections, ~96M transcripts, ~300K cells) from a 63-year-old melanoma patient using a custom 360-gene panel; spatially validated the HighMut (interfollicular epidermis) vs LowMut (hair follicle) melanocyte niche separation that was initially identified by in vitro single-cell genotyping and Smart-Seq2 RNA profiling PMID:39975212.

Notes

• Corpus-grown slug; not present in canonical ontology.
• In the ROBIN consortium, Xenium is used by the KIDSROBIN center (Harvard and UCSF) to spatially profile pediatric neuroblastoma tumors at single-cell resolution.
• KIDSROBIN positions Xenium profiling of genetically simple pediatric tumors (low TMB) as a tractable model for intra-tumoral heterogeneity with expected generalizability to adult cancers.
• Paired with 10x Visium HD for complementary transcriptome-wide spatial coverage in parallel tissue samples.

Sources

• PMID:41941260
• PMID:39975212

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