Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Evaluation of five different cDNA labeling methods for microarrays using spike controls.

Azadeh Badiee1, Hans Geir Eiken, Vidar M Steen

  • 1Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, University of Bergen, Bergen, Norway. azadeh.badiee@helse-bergen.no

BMC Biotechnology
|December 13, 2003
PubMed
Summary

Comparing five cDNA labeling methods for microarray analysis, direct labeling (CyScribe) and dendrimer technology (3DNA Array 50) demonstrated superior accuracy and reproducibility in detecting gene expression ratios.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

DNA methylation signatures associated with bipolar disorder in peripheral blood improve prediction models.

EBioMedicine·2026
Same author

Three-week effect of amisulpride, aripiprazole, and olanzapine on gene expression in peripheral blood in individuals with schizophrenia spectrum disorders.

The international journal of neuropsychopharmacology·2026
Same author

Aphid populations and virus vector potential in potato fields across seasons and regions in Norway.

Scientific reports·2025
Same author

Stabilization of human RNA and DNA in stool samples at room temperature.

BioTechniques·2025
Same author

Prednisolone add-on in early phase schizophrenia: A randomized, double-blind, placebo-controlled pilot study.

Brain, behavior, & immunity - health·2025
Same author

Penetrance of Neurodevelopmental Copy Number Variants Is Associated With Variations in Cortical Morphology.

Biological psychiatry. Cognitive neuroscience and neuroimaging·2025

Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Microarray gene expression analysis relies on accurate cDNA labeling.
  • Five commercial methods were evaluated: direct labeling (CyScribe), indirect labeling (FairPlay), dendrimer technology (3DNA Array 50 and 3DNA submicro), and hapten-antibody enzymatic labeling (Micromax TSA).
  • Spike mRNA controls were used against a total RNA background to assess performance.

Purpose of the Study:

  • To evaluate the accuracy and reproducibility of five distinct cDNA labeling techniques for microarray experiments.
  • To compare the performance of commercially available labeling kits under standardized conditions.
  • To identify optimal labeling methods for reliable gene expression profiling.

Main Methods:

  • Utilized ten spike controls with predetermined Cy5/Cy3 ratios (0.125 to 6.0).

Related Experiment Videos

  • Applied varying amounts of total RNA (5-50 microg) in labeling reactions.
  • Assessed labeling methods based on relative deviation from expected values, accuracy, and reproducibility.

    • Main Results:

    • 3DNA Array 50 (16% deviation) and CyScribe (17% deviation) exhibited the best accuracy and reproducibility.
    • FairPlay showed the lowest experimental variation (22%) but overestimated values (36%).
    • Micromax TSA displayed the highest variation (45%) and deviation (48%).

    Conclusions:

    • Spike controls are essential for validating and comparing cDNA labeling methods.
    • 3DNA Array 50 and CyScribe are recommended for accurate microarray gene expression analysis.
    • Method selection significantly impacts the reliability of gene expression data.