Publication
Title
Current annotation strategies for T cell phenotyping of single-cell RNA-seq data
Author
Abstract
Single-cell RNA sequencing (scRNA-seq) has become a popular technique for interrogating the diversity and dynamic nature of cellular gene expression and has numerous advantages in immunology. For example, scRNA-seq, in contrast to bulk RNA sequencing, can discern cellular subtypes within a population, which is important for heterogenous populations such as T cells. Moreover, recent advancements in the technology allow the parallel capturing of the highly diverse T-cell receptor (TCR) sequence with the gene expression. However, the field of single-cell RNA sequencing data analysis is still hampered by a lack of gold-standard cell phenotype annotation. This problem is particularly evident in the case of T cells due to the heterogeneity in both their gene expression and their TCR. While current cell phenotype annotation tools can differentiate major cell populations from each other, labelling T-cell subtypes remains problematic. In this review, we identify the common automated strategy for annotating T cells and their subpopulations, and also describe what crucial information is still missing from these tools.
Language
English
Source (journal)
Frontiers in immunology. - Place of publication unknown
Publication
Place of publication unknown : 2023
ISSN
1664-3224
DOI
10.3389/FIMMU.2023.1306169
Volume/pages
14 (2023) , p. 1-10
Article Reference
1306169
ISI
001135190900001
Pubmed ID
38187377
Full text (Publisher's DOI)
Full text (open access)
UAntwerpen
Faculty/Department
Research group
Project info
A framework to deduce the convoluted repertoire and epitope hierarchy of human T cell responses in visceral leishmaniasis: patient meets in silico.
Approaching multiple sclerosis from a computational perspective through bioinformatic analysis of the T-cell repertoire.
Single cell T-cell receptor and Expression Grouped Ontologies to develop a data-driven tool to identify T-cell immunity groups within a micro-environment and characterize the complex interplay of lymphocyte subtypes contributing to an immune response
Publication type
Subject
Affiliation
Publications with a UAntwerp address
External links
Record
Identifier
Creation 21.12.2023
Last edited 01.02.2024
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