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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...

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Updated: Jan 13, 2026

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

Massively Scalable Single-cell Multiomic Profiling of T Cell Repertoire with REFLEX.

Peter Skene¹, Matthew Hart¹, Zach Thomson¹

¹Allen Institute for Immunology, Seattle, WA, USA.

Research Square

|January 9, 2026

Summary

We developed REFLEX, a new high-throughput method for single-cell immune profiling. This technique enables scalable, cost-efficient multiomic analysis with paired T cell receptor sequencing, advancing adaptive immunity research.

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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

Published on: October 25, 2018

Area of Science:

Immunology
Genomics
Bioinformatics

Background:

Understanding T cell heterogeneity is crucial for analyzing immune responses.
Current single-cell technologies lack the throughput for complex immune repertoire studies.

Purpose of the Study:

To introduce REFLEX, a novel, scalable, and cost-efficient single-cell method.
To enable high-throughput multiomic profiling with paired T cell receptor (TCR) sequencing.

Main Methods:

REFLEX integrates in-situ reverse transcription and sample multiplexing barcodes.
It seamlessly combines with the 10x FLEX platform for enhanced data capture.
Profiling involved over 2 million cells from CMV-peptide-pulsed T cell expansions.

Main Results:

Successfully captured TCR sequences and multiomic data from 1.4 million T cells.
Identified numerous putative novel CMV-reactive clonotypes.
Demonstrated unprecedented scale and depth in T cell repertoire analysis.

Conclusions:

REFLEX significantly enhances the scale and depth of single-cell immune profiling.
The method offers transformative insights into T cell-mediated adaptive immunity.
REFLEX facilitates the discovery of antigen-specific T cell responses.