Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives.
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The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This review will summarize the development of various scRNA-seq technologies; primarily discussing the application of scRNA-seq on infectious diseases, and exploring the current development, challenges, and potential applications of scRNA-seq technology in the future.


3C, Chromosome Conformation Capture
ACE2, Angiotensin-Converting Enzyme 2
ARDS, acute respiratory distress syndrome
ATAC-seq, Assay for Transposase-Accessible Chromatin using sequencing
BCR, B cell receptor
CEL-seq, Cell Expression by Linear amplification and Sequencing
CLU, clusterin
COVID-19, corona virus disease 2019
CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
CytoSeq, gene expression cytometry
DENV, dengue virus
FACS, fluorescence-activated cell sorting
GNLY, granulysin
GO analysis, Gene Ontology analysis
HIV, Human Immunodeficiency Virus
IAV, Influenza A virus
IGHV/HD/HJ/HC, Immune globulin heavy V/D/J/C/ region
IGLV/LJ/LC, Immune globulin light V/J/C/ region
ILC, Innate Lymphoid Cell
Infectious diseases
LIGER, Linked Inference of Genomics Experimental Relationships
MAGIC, Markov Affinity-based Graph Imputation of Cells
MARS-seq, Massively parallel single-cell RNA sequencing
MATCHER, Manifold Alignment To CHaracterize Experimental Relationships
MCMV, mouse cytomegalovirus
MERFISH, Multiplexed, Error Robust Fluorescent In Situ Hybridization
MLV, Moloney Murine Leukemia Virus
MOFA, Multi-Omics Factor Analysis
MOI, multiplicity of infection
PBMCs, peripheral blood mononuclear cells
PLAC8, placenta-associated 8
SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
SAVER, Single-cell Analysis Via Expression Recovery
SPLit-seq, split pool ligation-based tranome sequencing
STARTRAC, Single T-cell Analysis by RNA sequencing and TCR TRACking
STRT-seq, Single-cell Tagged Reverse Transcription sequencing
Single-cell RNA sequencing
TCR, T cell receptor
TSLP, thymic stromal lymphopoietin
UMAP, Uniform Manifold Approximation and Projection
UMI, Unique Molecular Identifier
mcSCRB-seq, molecular crowding single-cell RNA barcoding and sequencing
pDCs, plasmacytoid dendritic cells
scRNA-seq, single cell RNA sequencing technology
sci-RNA-seq, single-cell combinatorial indexing RNA sequencing
seqFISH, sequential Fluorescent In Situ Hybridization
smart-seq, switching mechanism at 5′ end of the RNA transcript sequencing
t-SNE, t-Distributed stochastic neighbor embedding


Luo, Geyang
Gao, Qian
Zhang, Shuye
Yan, Bo

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