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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...

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Related Experiment Video

Updated: Jul 11, 2025

Simultaneous Quantification of T-Cell Receptor Excision Circles TRECs and K-Deleting Recombination Excision Circles KRECs by Real-time PCR

Simultaneous Quantification of T-Cell Receptor Excision Circles TRECs and K-Deleting Recombination Excision Circles KRECs by Real-time PCR

Published on: December 6, 2014

High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq.

Jasim Kada Benotmane^1,2,3, Jan Kueckelhaus^1,2,3, Paulina Will^1,2,3

¹Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.

Nature Communications

|November 17, 2023

Summary

Spatial T cell receptor sequencing (SPTCR-seq) enables detailed analysis of T cell dysfunction in cancer. This new method accurately reconstructs T cell receptor architecture, revealing immune cell interactions within tumors.

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Published on: May 25, 2015

Area of Science:

Immunology
Genomics
Cancer Research

Background:

Understanding T cell receptor (TCR) spatial distribution is crucial for cancer immunity.
Existing spatial transcriptomics lack direct TCR annotation capabilities.

Purpose of the Study:

Introduce spatially resolved T cell receptor sequencing (SPTCR-seq) for sensitive TCR sequencing.
Enable comprehensive analysis of T cell repertoire within the tumor microenvironment.

Main Methods:

SPTCR-seq integrates optimized target enrichment and long-read sequencing.
A dedicated computational pipeline (SPTCR) processes sequencing data.
Comparison with PCR-based methods to evaluate TCR reconstruction accuracy.

Main Results:

SPTCR-seq achieves high yield and coverage for TCR sequencing, comparable to single-cell methods.
SPTCR-seq excels at reconstructing the full TCR architecture, including V, D, J regions and CDR3.
Analysis revealed local T cell diversity, clonal expansion, and interactions with NK and B cells in T cell exhaustion.

Conclusions:

SPTCR-seq is a powerful tool for analyzing T cell dysfunction in cancer.
Integrating spatial omics with TCR sequencing provides novel insights into tumor immunology.
The method facilitates exploration of T cell behavior in various disease contexts.