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Related Concept Videos

RNA-seq03:21

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 microarray-based...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...

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Related Experiment Video

Updated: Jun 2, 2026

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
11:12

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material

Published on: August 1, 2018

mRNA transcript quantification in archival samples using multiplexed, color-coded probes.

Patricia P Reis1, Levi Waldron, Rashmi S Goswami

  • 1Division of Applied Molecular Oncology, Princess Margaret Hospital, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.

BMC Biotechnology
|May 10, 2011
PubMed
Summary
This summary is machine-generated.

The NanoString nCounter™ system offers accurate mRNA quantification in archived formalin-fixed, paraffin-embedded (FFPE) tissues. This probe-based technology outperforms quantitative real-time PCR (RQ-PCR) for gene expression analysis in FFPE samples.

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Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs
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Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs

Published on: April 14, 2015

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Last Updated: Jun 2, 2026

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
11:12

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Published on: August 1, 2018

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs
10:28

Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs

Published on: April 14, 2015

Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • A novel probe-based technology, the NanoString nCounter™ system, enables accurate mRNA quantification from limited total RNA.
  • This study evaluates the utility of NanoString for mRNA expression profiling in archived oral carcinoma tissues preserved in formalin-fixed, paraffin-embedded (FFPE) format.

Purpose of the Study:

  • To compare the performance of the NanoString nCounter™ system against quantitative real-time PCR (RQ-PCR) for mRNA expression analysis.
  • To assess the reliability of gene expression quantification in both fresh-frozen and FFPE oral carcinoma samples using both technologies.

Main Methods:

  • Gene expression of 20 target genes was quantified in 38 paired fresh-frozen and FFPE oral carcinoma samples using NanoString and SYBR Green I-based RQ-PCR.
  • Correlation analyses were performed to compare gene expression data between the two methods and between sample types (fresh-frozen vs. FFPE).

Main Results:

  • NanoString demonstrated a higher correlation (r=0.90) between fresh-frozen and FFPE samples compared to RQ-PCR (r=0.50).
  • Individual fresh-frozen and FFPE sample pairs showed a superior mean correlation with NanoString (r=0.94) versus RQ-PCR (r=0.53).
  • FFPE samples analyzed by RQ-PCR exhibited a lower overall correlation (0.59) compared to fresh-frozen samples (0.78), likely due to sample degradation.

Conclusions:

  • Both NanoString and RQ-PCR are viable for gene expression quantification in fresh-frozen and FFPE tissues.
  • The NanoString probe-based method provides superior gene expression quantification in archived FFPE samples compared to RQ-PCR.
  • The NanoString technique is well-suited for large-scale validation studies utilizing RNA from archived FFPE specimens.