Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

T Cell Activation and Clonal Selection

T Cell Activation and Clonal Selection

T cells are integral to our adaptive immune system, recognizing and effectively responding to foreign antigens. T cell activation and clonal selection are pivotal in orchestrating this immune response. This article elucidates these mechanisms, detailing the roles of cluster of differentiation (CD) markers, major histocompatibility complex (MHC) molecules, costimulatory signals, and the process of clonal selection.
Naive T cells that have not yet encountered an antigen express two primary CD...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

IL-17A deficiency in HLA-DR3 transgenic mice enriches beneficial Prevotella species in gut to promote Tregs and reduce CNS autoimmunity.

Microbiome·2026

Same author

Tumor-draining lymph nodes in ovarian cancer lack germinal centers but harbor tumor-reactive memory B cells clonally linked to intra-tumoral B cells.

Immunity·2026

Same author

Highly focused human CD8+ T-cell response in the lower airways during acute influenza infection.

Journal of immunology (Baltimore, Md. : 1950)·2026

Same author

Pre-transplant TCR Network Topology Predicts Kidney Allograft Rejection Independent of HLA Mismatch.

bioRxiv : the preprint server for biology·2026

Same author

Author Correction: Biallelic variants in the noncoding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes.

Nature genetics·2026

Same author

Saturation editing of RNU4-2 reveals distinct dominant and recessive disorders.

Nature·2026

Same journal

Editorial: Technologies for RNA Detection.

Bio-protocol·2026

Same journal

One-Step Affinity Purification of MarathonRT Reverse Transcriptase for RNA Sequencing Applications.

Bio-protocol·2026

Same journal

Enhanced RNA-Seq Expression Profiling and Functional Enrichment in Non-model Organisms Using Custom Annotations.

Bio-protocol·2026

Same journal

Using Combined Fluorescent In Situ Hybridization With Immunohistochemistry to Co-localize mRNA in Diverse Neuronal Cell Types.

Bio-protocol·2026

Same journal

Stepwise Protocol for Alternative Splicing Analysis in Single-Cell SMART-Seq2 RNA-Seq Data.

Bio-protocol·2026

Same journal

Enriching Bacteria-Specific RNA From Host Samples Before NGS With Transcript-Capture.

Bio-protocol·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 17, 2025

Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment

Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment

Published on: May 14, 2019

T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps.

Massimo Andreatta^1,2,3, Paul Gueguen^1,2,3, Nicholas Borcherding⁴

¹Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne, Epalinges, Switzerland.

|August 28, 2023

Summary

This summary is machine-generated.

This study introduces a computational workflow for analyzing T-cell states and clonotypes using single-cell RNA sequencing (scRNA-seq) and T-cell receptor (TCR) data. The method links T-cell clonality to their transcriptomic state, revealing relationships between clonal expansion and functional phenotypes.

Keywords:

Reference projection Single-cell analysis T-cell clone T-cell receptor TCR Transcriptomics scRNA-seq scTCR-seq

More Related Videos

T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing

T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing

Published on: January 12, 2021

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Related Experiment Videos

Last Updated: Jul 17, 2025

Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment

Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment

Published on: May 14, 2019

T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing

T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing

Published on: January 12, 2021

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Area of Science:

Immunology
Computational Biology
Bioinformatics

Background:

T cells utilize T-cell receptors (TCRs) for antigen recognition, enabling adaptive immune responses.
Distinct TCR sequences act as molecular barcodes for tracking T cell clonotypes.
Single-cell RNA sequencing (scRNA-seq) offers coupled TCR and transcriptional data for detailed T cell analysis.

Purpose of the Study:

To present a computational workflow for integrated T-cell state and clonal analysis from scRNA-seq data.
To enable the characterization of T-cell functional states and clonal structures.
To link T-cell clonality with transcriptomic profiles for deeper biological insights.

Main Methods:

Utilizes R packages Seurat, ProjecTILs, and scRepertoire for data analysis.
Employs reference projection with ProjecTILs for automated T-cell state annotation.
Integrates scRNA-seq and TCR sequencing data for comprehensive clonotype tracking.

Main Results:

The workflow allows for automated annotation of T-cell functional states.
Enables detailed tracking of individual T-cell clonotypes, including expansion and proliferation.
Facilitates the assessment of clonal overlap between different T-cell subtypes.
Links clonal expansion and differentiation states to functional phenotypes.

Conclusions:

The presented computational workflow provides a reproducible method for analyzing T-cell states and clonality.
This approach enhances the understanding of T-cell responses by integrating transcriptomic and TCR repertoire data.
The findings support the use of scRNA-seq and computational tools for dissecting adaptive immunity.