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Related Concept Videos

RNA-seq03:21

RNA-seq

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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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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Related Experiment Video

Updated: Jan 10, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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Protocol to track single-cell-derived clones using DNA barcoding combined with single-cell RNA sequencing.

Hee Jin Shin1, Sahil Sharma2, Sarah Kronheim2

  • 1Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.

STAR Protocols
|November 29, 2025
PubMed
Summary

This study presents a new protocol for tracking cell clones using DNA barcodes and single-cell RNA sequencing. This method links clone growth to gene expression, aiding cancer research.

Keywords:
CancerCell BiologyRNA-seqSequence analysisSequencingSingle Cell

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Area of Science:

  • Oncology
  • Molecular Biology
  • Genetics

Background:

  • Tumor heterogeneity, driven by clonal fitness and plasticity, contributes to cancer progression and treatment resistance.
  • Understanding clonal dynamics is crucial for developing effective cancer therapies.

Purpose of the Study:

  • To provide a detailed protocol for tracking clonal outputs from uniquely marked cells.
  • To link clonal growth activity with transcriptomic profiles for deeper biological insights.

Main Methods:

  • Construction and validation of lentiviral DNA barcode libraries.
  • Single-cell RNA sequencing (scRNA-seq) to analyze transcriptomic profiles.
  • Permanent cellular labeling for long-term clonal tracking.

Main Results:

  • The protocol enables the permanent labeling of cells with unique DNA barcodes.
  • It successfully links clonal growth and expansion to specific transcriptomic signatures.
  • This approach facilitates the study of clonal dynamics in various model systems.

Conclusions:

  • This protocol offers a powerful tool for investigating the molecular mechanisms of clone function in cancer.
  • It provides insights into tumor heterogeneity, disease progression, and treatment resistance.
  • The method supports the development of targeted cancer therapies by elucidating clonal behavior.