What Are Your T Cells Really Doing? A Journey Through TCR Single-Cell Data and Epitope Annotation

T cells don’t just patrol the immune system; they remember, recognize, and respond. At the center of this ability is the T cell receptor (TCR), a molecular antenna tuned to detect antigens (depicted on the right). For years, deciphering the behavior of individual T cells was like trying to follow a conversation in a noisy room: possible in fragments, but far from clear.

Advances in TCR-coupled single-cell RNA sequencing have changed that. This approach now allows us to capture each T cell in high resolution, connect its transcriptional profile to its unique TCR sequence, and map it within the broader immune landscape.

In this post, written by Single Cell Discoveries, we will guide you through a comprehensive analysis journey, from UMAP clustering to clonotype tracking and epitope annotation, revealing how T cells behave, interact, and respond to their environment.

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