☆ 4.5 Article

Single-cell RNA sequencing analyses: interference by the genes that encode the B-cell and T-cell receptors

BRIEFINGS IN FUNCTIONAL GENOMICS (2023)

Related references

Note: Only part of the references are listed.

Article Immunology

Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood

Jacqueline H. Y. Siu et al.

Summary: This study provides a deep analysis of B cells in lymphoid tissues and blood of deceased organ donors, leading to the identification of two subsets of marginal zone B (MZB) cells with distinct features and roles in immune response and pathology, emphasizing the importance of considering MZB cell heterogeneity in studying human B cell responses.

SCIENCE IMMUNOLOGY (2022)

Add to Collection

Article Biology

A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections

Massimo Andreatta et al.

Summary: This study utilized single-cell transcriptomics to characterize the diversity of CD4(+) T cells responding to viral infections and built a comprehensive map of their transcriptional states. The research revealed the progressive changes in CD4(+) T cell subtypes during acute infections and identified distinct programs associated with chronic infections. Additionally, the study demonstrated the private nature of virus-specific CD4(+) T cell responses across individuals and their differentiation into Tfh and Th1 subtypes. Moreover, the CD4(+) T cell map developed in this study can be used to interpret cell states in other single-cell datasets.

ELIFE (2022)

Add to Collection

Article Immunology

Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics

Hamish W. King et al.

Summary: Our study provides a comprehensive roadmap of human B cell maturation by analyzing single-cell transcriptomics and antibody repertoires, revealing the heterogeneity of memory B cells with diverse functional and signaling states. We reconstruct gene expression dynamics during B cell activation, showing a pre-germinal center state prepared for class switch recombination, and dissect how antibody class-dependent gene expression in germinal center and memory B cells is linked with potential fate and function influence. Our analyses uncover the dynamic cellular states that shape human B cell-mediated immunity, emphasizing the potential role of antibody isotype during antibody-based selection.

SCIENCE IMMUNOLOGY (2021)

Add to Collection

Article Immunology

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways

Alexander Stewart et al.

Summary: The separation of B cells into different subsets has provided insights into their diverse functions in immune responses. Advances in single-cell techniques have enabled a deeper understanding of B cell characteristics and functions, though challenges remain. This study offers a reference single-cell dataset for better classification of functional B cell subsets in peripheral blood, highlighting the complexity and diversity of B cell populations.

FRONTIERS IN IMMUNOLOGY (2021)

Add to Collection

Article Biochemistry & Molecular Biology

Integrated analysis of multimodal single-cell data

Yuhan Hao et al.

Summary: The study introduces a weighted-nearest neighbor analysis framework to learn the relative utility of each data type in each cell, enabling integrative analysis of multiple modalities. Applied to a CITE-seq dataset, the method constructs a multimodal reference atlas of the circulating immune system and successfully identifies and validates previously unreported lymphoid subpopulations.

CELL (2021)

Add to Collection

Article Cell Biology

Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells

Nimitha R. Mathew et al.

Summary: The study identified differences in antigen-specific B cell responses in lymphoid organs, spleen, and lungs after infection, as well as germinal center B cell subpopulations in different organs. Transcriptional differences were found between memory cells in lungs and lymphoid organs, and organ-restricted clonal expansion was observed. Furthermore, significant clonal overlap between germinal center-derived memory and plasma cells was discovered.

CELL REPORTS (2021)

Add to Collection

Article Immunology

Two subsets of stem-like CD8+memory T cell progenitors with distinct fate commitments in humans

Giovanni Galletti et al.

NATURE IMMUNOLOGY (2020)

Add to Collection

Article Multidisciplinary Sciences

Integrative transcriptome and chromatin landscape analysis reveals distinct epigenetic regulations in human memory B cells

Justin B. Moroney et al.

NATURE COMMUNICATIONS (2020)

Add to Collection

Article Multidisciplinary Sciences

The single-cell transcriptional landscape of mammalian organogenesis

Junyue Cao et al.

NATURE (2019)

Add to Collection

Article Biotechnology & Applied Microbiology

Dimensionality reduction for visualizing single-cell data using UMAP

Etienne Becht et al.

NATURE BIOTECHNOLOGY (2019)

Add to Collection

Article Biotechnology & Applied Microbiology

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Christoph Hafemeister et al.

GENOME BIOLOGY (2019)

Add to Collection

Article Immunology

Dissecting Integrin Expression and Function on Memory B Cells in Mice and Humans in Autoimmunity

Alessandro Camponeschi et al.

FRONTIERS IN IMMUNOLOGY (2019)

Add to Collection

Article Biology

Clustering trees: a visualization for evaluating clusterings at multiple resolutions

Luke Zappia et al.

GIGASCIENCE (2018)

Add to Collection

Review Immunology

Defining Memory CD8 T Cell

Matthew D. Martin et al.

FRONTIERS IN IMMUNOLOGY (2018)

Add to Collection

Article Biochemical Research Methods

Reversed graph embedding resolves complex single-cell trajectories

Xiaojie Qiu et al.

NATURE METHODS (2017)

Add to Collection

Article Biotechnology & Applied Microbiology

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Cole Trapnell et al.

NATURE BIOTECHNOLOGY (2014)

Add to Collection

Article Biochemistry & Molecular Biology

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

J. Douglas Freeman et al.

GENOME RESEARCH (2009)

Add to Collection

Article Fisheries

Similarity and divergence in the development and expression of the mouse and human antibody repertoires

HW Schroeder

DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY (2006)

Add to Collection

© Peeref 2019-2024. All rights reserved.