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Journal of Bacteriology, December 2001, p. 7371-7380, Vol. 183, No. 24
0021-9193/01/$04.00+0   DOI: 10.1128/JB.183.24.7371-7380.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

RNA Expression Analysis Using an Antisense Bacillus subtilis Genome Array

Jian-Ming Lee,dagger Shehui Zhang, Soumitra Saha, Sonia Santa Anna, Can Jiang, and John Perkins*

Roche Vitamins Inc., Nutley, New Jersey 07110

Received 6 July 2001/Accepted 19 September 2001

We have developed an antisense oligonucleotide microarray for the study of gene expression and regulation in Bacillus subtilis by using Affymetrix technology. Quality control tests of the B. subtilis GeneChip were performed to ascertain the quality of the array. These tests included optimization of the labeling and hybridization conditions, determination of the linear dynamic range of gene expression levels, and assessment of differential gene expression patterns of known vitamin biosynthetic genes. In minimal medium, we detected transcripts for approximately 70% of the known open reading frames (ORFs). In addition, we were able to monitor the transcript level of known biosynthetic genes regulated by riboflavin, biotin, or thiamine. Moreover, novel transcripts were also detected within intergenic regions and on the opposite coding strand of known ORFs. Several of these novel transcripts were subsequently correlated to new coding regions.

* Corresponding author. Mailing address: F. Hoffmann-La Roche, Ltd., Department VFB, Bldg. 203/20A, CH-4070 Basel, Switzerland. Phone: 41-61-687-2325. Fax: 41-61-687-4727. E-mail: john.perkins{at}roche.com.

dagger Present address: Unilever Research, U.S., Edgewater, NJ 07020.

Journal of Bacteriology, December 2001, p. 7371-7380, Vol. 183, No. 24
0021-9193/01/$04.00+0   DOI: 10.1128/JB.183.24.7371-7380.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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