Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information
Yian Ann Chen,David J. McKillen,Shuyuan Wu,Matthew J. Jenny,R. W. Chapman,R. W. Chapman,Paul S. Gross,Gregory W. Warr,Jonas S. Almeida +8 more
TL;DR: A general design procedure to select a subset of ESTs that will minimize sequence redundancy and characterize potential cross-hybridization while providing functionally representative probes is described.
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Abstract: Background
Expression microarrays are increasingly used to characterize environmental responses and host-parasite interactions for many different organisms. Probe selection for cDNA microarrays using expressed sequence tags (ESTs) is challenging due to high sequence redundancy and potential cross-hybridization between paralogous genes. In organisms with limited genomic information, like marine organisms, this challenge is even greater due to annotation uncertainty. No general tool is available for cDNA microarray probe selection for these organisms. Therefore, the goal of the design procedure described here is to select a subset of ESTs that will minimize sequence redundancy and characterize potential cross-hybridization while providing functionally representative probes.
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The molecular ecologist's guide to expressed sequence tags
TL;DR: How ESTs have been used in molecular ecology research in the last several years by providing sequence data for the design of molecular markers, genome‐wide studies of gene expression and selection, the identification of candidate genes underlying adaptation, and the basis for Studies of gene family and genome evolution are reviewed.
501
A cDNA microarray for Crassostrea virginica and C. gigas.
Matthew J. Jenny,Robert W. Chapman,Annalaura Mancia,Yian A. Chen,David J. McKillen,Hal Trent,Paul Lang,Jean Michel Escoubas,Evelyne Bachère,Viviane Boulo,Z. John Liu,Paul S. Gross,Charles E. Cunningham,Pauline M. Cupit,Arnaud Tanguy,Ximing Guo,Dario Moraga,Isabelle Boutet,Arnaud Huvet,Sylvain De Guise,Jonas S. Almeida,Gregory W. Warr +21 more
TL;DR: An international group of collaborators has constructed a 27,496-feature cDNA microarray containing 4460 sequences derived from C. virginica and C. gigas, and the correlation between hybridization intensity and sequence homology for selected genes determined.
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Core oxidative stress response in Aspergillus nidulans
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A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions.
Annalaura Mancia,Mats L. Lundqvist,Mats L. Lundqvist,Tracy A. Romano,Margie M. Peden-Adams,Patricia A. Fair,Patricia A. Fair,Mark S. Kindy,Blake C. Ellis,Sebastiano Gattoni-Celli,David J. McKillen,Harold F. Trent,Yian Ann Chen,Jonas S. Almeida,Paul S. Gross,Robert W. Chapman,Gregory W. Warr +16 more
TL;DR: The results demonstrate that the array is a reproducible and informative tool for assessing differential gene expression in dolphin PBL and in other tissues.
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