Prediction of cell position using single-cell transcriptomic data: an iterative procedure.

Abstract

Single-cell sequencing reveals cellular heterogeneity but not cell localization. However, by combining single-cell transcriptomic data with a reference atlas of a small set of genes, it would be possible to predict the position of individual cells and reconstruct the spatial expression profile of thousands of genes reported in the single-cell study. To develop new algorithms for this purpose, the Dialogue for Reverse Engineering Assessments and Methods (DREAM) consortium organized a crowd-sourced competition known as DREAM Single Cell Transcriptomics Challenge (SCTC). In the spirit of this framework, we describe here the proposed procedures for adequate reference genes selection, and an iterative procedure to predict spatial expression profile of other genes.

Keywords

Spatial Gene Expression
Spatial Omics
Spatial reconstruction
smFISH
DREAM Challenge
Drosophila Embryo
Gene expression Patterns
Single-Cell RNA sequencing

Authors

Alonso, Andrés M
Carrea, Alejandra
Diambra, Luis

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