Expanding Gene Expression profile in Targeted Spatial Transcriptomics through scRNA-seq data integration

Rahul Tyagi, Vaibhav Mittal, Riya Podder, Sumanth Reddy

Keywords: Gene Expression, Spatial data, Spatial Transcriptomics, Targeted Transcriptomics, scRNA-seq, data integration

TL;DR: Expanding Gene Expression profile in Targeted Spatial Transcriptomics through scRNA-seq data integration

Abstract:

We present an improved methodology for gene expression imputation (GEI) in Xenium, a
targeted spatial transcriptomics platform. Xenium provides single-cell resolution but measures
only a limited set of genes, restricting downstream analyses. Our approach of aligning spatial
and reference scRNA-seq data through “Symphony” in a common embedding space, integrating
them using single-cell neighborhood information improved recovery of genome-wide expression
profiles from targeted panels, enabling more accurate downstream analysis.

Submission Number: 11