Optimization of cDNA-AFLP experiments using genomic sequence data

Teemu Kivioja, Mikko Arvas, Markku Saloheimo, Merja Penttilä, Esko Ukkonen

Research output: Contribution to journalArticleScientificpeer-review

18 Citations (Scopus)

Abstract

Motivation: cDNA amplified fragment length polymorphism (cDNA-AFLP) is one of the few genome-wide level expression profiling methods capable of finding genes that have not yet been cloned or even predicted from sequence but have interesting expression patterns under the studied conditions. In cDNA-AFLP, a complex cDNA mixture is divided into small subsets using restriction enzymes and selective PCR. A large cDNA-AFLP experiment can require a substantial amount of resources, such as hundreds of PCR amplifications and gel electrophoresis runs, followed by manual cutting of a large number of bands from the gels. Our aim was to test whether this workload can be reduced by rational design of the experiment. Results: We used the available genomic sequence information to optimize cDNA-AFLP experiments beforehand so that as many transcripts as possible could be profiled with a given amount of resources. Optimization of the selection of both restriction enzymes and selective primers for cDNA-AFLP experiments has not been performed previously. The in silico tests performed suggest that substantial amounts of resources can be saved by the optimization of cDNA-AFLP experiments.

Original languageEnglish
Pages (from-to)2573-2579
Number of pages7
JournalBioinformatics
Volume21
Issue number11
DOIs
Publication statusPublished - 1 Jun 2005
MoE publication typeA1 Journal article-refereed

Fingerprint

Polymorphism
CDNA
Genomics
Fragment
Complementary DNA
Optimization
Experiment
Experiments
Gels
Enzymes
Resources
Genes
Restriction
Polymerase Chain Reaction
Electrophoresis
Amplification
Profiling
Workload
Complex Mixtures
Computer Simulation

Keywords

  • cDNA microarrays
  • amplified fragment length polymorphism
  • AFLP
  • gene expression
  • genome-wide expression analysis

Cite this

Kivioja, Teemu ; Arvas, Mikko ; Saloheimo, Markku ; Penttilä, Merja ; Ukkonen, Esko. / Optimization of cDNA-AFLP experiments using genomic sequence data. In: Bioinformatics. 2005 ; Vol. 21, No. 11. pp. 2573-2579.
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Optimization of cDNA-AFLP experiments using genomic sequence data. / Kivioja, Teemu; Arvas, Mikko; Saloheimo, Markku; Penttilä, Merja; Ukkonen, Esko.

In: Bioinformatics, Vol. 21, No. 11, 01.06.2005, p. 2573-2579.

Research output: Contribution to journalArticleScientificpeer-review

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