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 language | English |
|---|---|
| Pages (from-to) | 2573-2579 |
| Number of pages | 7 |
| Journal | Bioinformatics |
| Volume | 21 |
| Issue number | 11 |
| DOIs | |
| Publication status | Published - 1 Jun 2005 |
| MoE publication type | A1 Journal article-refereed |
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Keywords
- cDNA microarrays
- amplified fragment length polymorphism
- AFLP
- gene expression
- genome-wide expression analysis
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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 journal › Article › Scientific › peer-review
TY - JOUR
T1 - Optimization of cDNA-AFLP experiments using genomic sequence data
AU - Kivioja, Teemu
AU - Arvas, Mikko
AU - Saloheimo, Markku
AU - Penttilä, Merja
AU - Ukkonen, Esko
PY - 2005/6/1
Y1 - 2005/6/1
N2 - 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.
AB - 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.
KW - cDNA microarrays
KW - amplified fragment length polymorphism
KW - AFLP
KW - gene expression
KW - genome-wide expression analysis
UR - http://www.scopus.com/inward/record.url?scp=20744449338&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/bti393
DO - 10.1093/bioinformatics/bti393
M3 - Article
C2 - 15774551
AN - SCOPUS:20744449338
VL - 21
SP - 2573
EP - 2579
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 11
ER -