SpaGE: Spatial Gene Enhancement using scRNA-seq.

IF: 19.160

Cited by: 71

Abstract

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 some methods 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 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 using in situ hybridization data from the Allen Mouse Brain Atlas.

Keywords

Spatial Transcriptomics

MeSH terms

Animals

Databases, Genetic

Datasets as Topic

Mice

RNA-Seq

Single-Cell Analysis

Software

Transcriptome

Authors

Abdelaal, Tamim

Mourragui, Soufiane

Mahfouz, Ahmed

Reinders, Marcel J T

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