Current Genetics

, Volume 49, Issue 2, pp 106–124

Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii

  • Stephan Eberhard
  • Monica Jain
  • Chung Soon Im
  • Steve Pollock
  • Jeff Shrager
  • Yuan Lin
  • Andrew S. Peek
  • Arthur R. Grossman
Research Article

Abstract

The availability of genome sequences makes it possible to develop microarrays that can be used for profiling gene expression over developmental time, as organisms respond to environmental challenges, and for comparison between wild-type and mutant strains under various conditions. The desired characteristics of microarrays (intense signals, hybridization specificity and extensive coverage of the transcriptome) were not fully met by the previous Chlamydomonas reinhardtii microarray: probes derived from cDNA sequences (~300 bp) were prone to some nonspecific cross-hybridization and coverage of the transcriptome was only ~20%. The near completion of the C. reinhardtii nuclear genome sequence and the availability of extensive cDNA information have made it feasible to improve upon these aspects. After developing a protocol for selecting a high-quality unigene set representing all known expressed sequences, oligonucleotides were designed and a microarray with ~10,000 unique array elements (~70 bp) covering 87% of the known transcriptome was developed. This microarray will enable researchers to generate a global view of gene expression in C. reinhardtii. Furthermore, the detailed description of the protocol for selecting a unigene set and the design of oligonucleotides may be of interest for laboratories interested in developing microarrays for organisms whose genome sequences are not yet completed (but are nearing completion).

Keywords

Chlamydomonas Gene expression Oligo-array Genomics 

Supplementary material

294_2005_41_MOESM1_ESM.pdf (26 kb)
Supplementary material

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Stephan Eberhard
    • 1
    • 2
  • Monica Jain
    • 1
  • Chung Soon Im
    • 1
  • Steve Pollock
    • 1
  • Jeff Shrager
    • 1
  • Yuan Lin
    • 3
  • Andrew S. Peek
    • 3
  • Arthur R. Grossman
    • 1
  1. 1.Department of Plant BiologyThe Carnegie InstitutionStanfordUSA
  2. 2.Laboratoire de Physiologie Moléculaire et Membranaire du Chloroplaste, Institut de Biologie Physico-ChimiqueUMR7141 (CNRS – Université Paris VI)ParisFrance
  3. 3.Integrated DNA TechnologiesCoralvilleUSA

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