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Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST.
Zhi-Jie Cao1, Lin Wei1, Shen Lu1
1Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, 100871, Beijing, China.
Nature Communications
|July 12, 2020
Summary
Cell BLAST is a new tool for annotating single-cell RNA sequencing (scRNA-seq) data. It accurately queries and curates newly sequenced cells by measuring cell similarity and handling batch effects.
Area of Science:
- Genomics
- Computational Biology
- Bioinformatics
Background:
- Single-cell RNA sequencing (scRNA-seq) is crucial for understanding cellular heterogeneity.
- The increasing volume of public scRNA-seq data necessitates efficient cell-querying methods.
- Accurate cell-to-cell similarity measures and robust batch effect handling are vital for data utilization.
Purpose of the Study:
- To develop an accurate and robust cell-querying method for scRNA-seq data analysis.
- To enable effective utilization of existing annotations for newly sequenced cells.
- To provide a comprehensive solution for cell type annotation and differentiation potential assessment.
Main Methods:
- Development of Cell BLAST, a novel cell-querying method.
- Utilizing a neural network-based generative model for data analysis.
- Implementing a customized cell-to-cell similarity metric to address batch effects.
Main Results:
- Cell BLAST demonstrates high accuracy in annotating discrete cell types.
- The method effectively assesses continuous cell differentiation potential.
- Cell BLAST successfully identifies novel cell types within scRNA-seq datasets.
- Extensive benchmarks and case studies validate the tool's performance.
Conclusions:
- Cell BLAST offers an accurate and robust solution for scRNA-seq cell querying and annotation.
- The tool facilitates the curation of newly sequenced cells using public annotations.
- Cell BLAST, integrated with a reference database and web server, provides a user-friendly platform for real-world applications.
