Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2.

Publication date: Jul 17, 2023

The recent emergence of multi-sample multi-condition single-cell multi-cohort studies allows researchers to investigate different cell states. The effective integration of multiple large-cohort studies promises biological insights into cells under different conditions that individual studies cannot provide. Here, we present scMerge2, a scalable algorithm that allows data integration of atlas-scale multi-sample multi-condition single-cell studies. We have generalized scMerge2 to enable the merging of millions of cells from single-cell studies generated by various single-cell technologies. Using a large COVID-19 data collection with over five million cells from 1000+ individuals, we demonstrate that scMerge2 enables multi-sample multi-condition scRNA-seq data integration from multiple cohorts and reveals signatures derived from cell-type expression that are more accurate in discriminating disease progression. Further, we demonstrate that scMerge2 can remove dataset variability in CyTOF, imaging mass cytometry and CITE-seq experiments, demonstrating its applicability to a broad spectrum of single-cell profiling technologies.

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Concepts Keywords
Accurate Atlas
Atlas Cell
Cytometry Cohort
Scmerge2 Condition


Type Source Name
disease IDO cell
disease VO effective
disease IDO algorithm
disease MESH COVID-19
disease MESH disease progression
disease VO time
disease IDO replication
disease VO effectiveness
drug DRUGBANK Isoxaflutole
disease VO efficiency
disease VO efficient
disease VO protocol
drug DRUGBANK Pidolic Acid
disease MESH critical illness
disease IDO biological process
disease IDO production
drug DRUGBANK Sulpiride
disease MESH sepsis
pathway REACTOME Oxidative Stress Induced Senescence
pathway KEGG Oxidative phosphorylation
pathway KEGG Chemokine signaling pathway
pathway KEGG Ribosome
pathway KEGG Apoptosis
disease IDO symptom
drug DRUGBANK Aspartame
disease VO gene
drug DRUGBANK Coenzyme M
drug DRUGBANK N-Cyclohexyltaurine

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