Design, Optimization and Validation of Genomic DNA Microarrays for Examining the Clostridium acetobutylicum Transcriptome

• Published in: Biotechnology and bioprocess engineering Vol. 10; no. 5
• Main Authors: Alsaker, Keith V. (Northwestern University, Evanston, IL, USA), Paredes, Carlos J. (Northwestern University, Evanston, IL, USA), Papoutsakis, Eleftherios T. (Northwestern University, Evanston, IL, USA), E-mail: e-paps@northwestern.edu
• Format: Journal Article
• Language: English
• Published: 01.09.2005
• Subjects: AbrB; BUTANOL; CHOC; degenerate strain; diffusion limitation; ESPORULACION; ESTRES TERMICO; EXPRESION GENICA; EXPRESSION DES GENES; extrachromosomal; GENE EXPRESSION; gram-positive; HEAT STRESS; microarray design; number-of-expressed-genes; SHOCK; solvent-production; Spo0A; SPORULATION; STRESS THERMIQUE
• ISSN: 1226-8372; 1976-3816
• DOI: 10.1007/BF02989826

Microarray technology has contributed significantly to the understanding of bacterial genetics and transcriptional regulation. One neglected aspect of this technology has been optimization of microarray-generated signals and quality of generated information. Full genome microarrays were developed for Clostridium acetobutylicum through spotting of PCR products that were designed with minimal homology with all other genes within the genome. Using statistical analysis it is demonstrated that signal quality is significantly improved by increasing the hybridization volume, possibly increasing the effective number of transcripts available to bind to a given spot, while changes in labeled probe amounts were found to be less sensitive to improving signal quality.