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 Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

You might also read

Related Articles

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

Sort by
Same author

Impact of interspecies colostrum and milk replacement on circulating sncRNA dynamics of neonatal goat kids.

RNA biology·2026
Same author

Extreme GC3 codon bias in a novel brown seaweed virus results in pseudoambigrammatic characteristics.

Virus evolution·2026
Same author

Evaluation of RNA extraction and rRNA depletion protocols for RNA-Seq in eleven edible seaweed species from brown, red, and green algae.

PloS one·2026
Same author

Discovery of a new konkovirus species in <i>Lachenalia</i> plants reveals possible co-evolution between 5' and 3' RNA sequence motifs.

The Journal of general virology·2025
Same author

<i>Candida albicans</i> and <i>Staphylococcus aureus</i> reciprocally promote their virulence factor secretion and pro-inflammatory effects.

Frontiers in cellular and infection microbiology·2025
Same author

Role of RelA-synthesized (p)ppGpp and ROS-induced mutagenesis in <i>de novo</i> acquisition of antibiotic resistance in <i>E. coli</i>.

iScience·2024

Related Experiment Video

Updated: Jul 2, 2026

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
13:19

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer

Published on: November 2, 2013

Salvaging Affymetrix probes after probe-level re-annotation.

Wim C de Leeuw1, Han Rauwerda, Martijs J Jonker

  • 1MicroArray Department & Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, the Netherlands. w.c.deleeuw@uva.nl

BMC Research Notes
|August 20, 2008
PubMed
Summary
This summary is machine-generated.

Re-annotating Affymetrix GeneChips with custom Chip Description Files (CDFs) can lose probes. Our CDF-Merger algorithm salvages up to 94% of lost probes, restoring valuable gene expression data.

More Related Videos

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos
13:54

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

Published on: October 10, 2011

Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

Related Experiment Videos

Last Updated: Jul 2, 2026

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
13:19

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer

Published on: November 2, 2013

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos
13:54

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

Published on: October 10, 2011

Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

Area of Science:

  • Genomics
  • Bioinformatics
  • Gene Expression Analysis

Background:

  • Affymetrix GeneChips are re-annotated using custom Chip Description Files (CDFs) for improved data quality.
  • This re-annotation process results in the loss of 44-71% of probes, leading to significant data loss.
  • Biologists are hesitant to adopt custom CDFs due to the substantial loss of experimental data.

Purpose of the Study:

  • To re-introduce lost Affymetrix probe-sets after re-annotation procedures.
  • To develop a method for salvaging probes lost during custom CDF creation.
  • To enhance the utility and data recovery of Affymetrix GeneChip experiments.

Main Methods:

  • Developed the CDF-Merger algorithm to re-introduce non-affected probe-sets.
  • Applied CDF-Merger to standard Affymetrix CDFs and custom Brainarray CDFs.
  • Created Hybrid CDFs by merging standard and custom annotations.

Main Results:

  • The CDF-Merger algorithm restored probe content up to 94%.
  • Salvaged probes, representing up to 54% of array content, were made traceable.
  • Ensured biologists can select probe-sets based on origin and reliability during analysis.

Conclusions:

  • The developed Hybrid CDFs and R environment facilitate easy implementation of the probe-salvaging approach.
  • This method significantly improves data recovery in gene expression studies using re-annotated Affymetrix GeneChips.