SpaGE: Spatial Gene Enhancement using scRNA-seq

Research output: Contribution to journalArticleScientificpeer-review

4 Downloads (Pure)

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.

Original languageEnglish
Article numbere107
Number of pages17
JournalNucleic Acids Research
Volume48
Issue number18
DOIs
Publication statusPublished - 2020

Keywords

  • OA-Fund TU Delft

Fingerprint Dive into the research topics of 'SpaGE: Spatial Gene Enhancement using scRNA-seq'. Together they form a unique fingerprint.

Cite this