SpaGE: Spatial Gene Enhancement using scRNA-seq [article]

Tamim Abdelaal, Soufiane Mourragui, Ahmed Mahfouz, Marcel Reinders
2020 bioRxiv   pre-print
Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome expression of single cells, it lacks their spatial localization. Novel spatial transcriptomics methods do retain cells spatial information but can only measure tens to hundreds of transcripts. To resolve this discrepancy, we developed SpaGE, a method that integrates spatial and scRNA-seq datasets to predict
more » ... ts to predict whole-transcriptome expressions in their spatial configuration. Using five dataset-pairs, SpaGE outperformed previously published methods and showed scalability to large datasets. Moreover, SpaGE predicted new spatial gene patterns that are confirmed independently.
doi:10.1101/2020.05.08.084392 fatcat:f2b5vmh5sbhxvf2qyq2mbxok5e