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An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences

Jacob Pollier UGent, Miguel Gonzalez Guzman UGent, Wilson Ardiles Diaz UGent, Danny Geelen UGent and Alain Goossens UGent (2011) PLOS ONE. 6(9).
abstract
Background: cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. Methodology: A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. Conclusions: The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
GENOME-WIDE EXPRESSION, FAMILY, AMPLIFICATION, AFLP
journal title
PLOS ONE
PLoS One
volume
6
issue
9
article_number
e24978
pages
6 pages
Web of Science type
Article
Web of Science id
000295041700085
JCR category
BIOLOGY
JCR impact factor
4.092 (2011)
JCR rank
12/84 (2011)
JCR quartile
1 (2011)
ISSN
1932-6203
DOI
10.1371/journal.pone.0024978
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
1939649
handle
http://hdl.handle.net/1854/LU-1939649
date created
2011-11-07 17:36:22
date last changed
2011-11-08 12:21:57
@article{1939649,
  abstract     = {Background: cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis.
Methodology: A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67\%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts.
Conclusions: The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.},
  articleno    = {e24978},
  author       = {Pollier, Jacob and Gonzalez Guzman, Miguel and Ardiles Diaz, Wilson and Geelen, Danny and Goossens, Alain},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {GENOME-WIDE EXPRESSION,FAMILY,AMPLIFICATION,AFLP},
  language     = {eng},
  number       = {9},
  pages        = {6},
  title        = {An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences},
  url          = {http://dx.doi.org/10.1371/journal.pone.0024978},
  volume       = {6},
  year         = {2011},
}

Chicago
Pollier, Jacob, Miguel Gonzalez Guzman, Wilson Ardiles Diaz, Danny Geelen, and Alain Goossens. 2011. “An Integrated PCR Colony Hybridization Approach to Screen cDNA Libraries for Full-length Coding Sequences.” Plos One 6 (9).
APA
Pollier, J., Gonzalez Guzman, M., Ardiles Diaz, W., Geelen, D., & Goossens, A. (2011). An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences. PLOS ONE, 6(9).
Vancouver
1.
Pollier J, Gonzalez Guzman M, Ardiles Diaz W, Geelen D, Goossens A. An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences. PLOS ONE. 2011;6(9).
MLA
Pollier, Jacob, Miguel Gonzalez Guzman, Wilson Ardiles Diaz, et al. “An Integrated PCR Colony Hybridization Approach to Screen cDNA Libraries for Full-length Coding Sequences.” PLOS ONE 6.9 (2011): n. pag. Print.