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Nucleic Acids Research, 2002, Vol. 30, No. 17 3732-3738
© 2002 Oxford University Press

Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays

Brian Tjaden, Rini Mukherjee Saxena1, Sergey Stolyar2, David R. Haynor3, Eugene Kolker2 and Carsten Rosenow*,1

Department of Computer Science, University of Washington, Seattle, WA 98195, USA, 1 Affymetrix Inc., 3380 Central Expressway, Santa Clara, CA 95051, USA, 2 Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA and 3 Department of Radiology, University of Washington, Seattle, WA 98195, USA

*To whom correspondence should be addressed. Tel: +1 408 731 5024; Fax: +1 408 481 0422; Email: carsten_rosenow{at}affymetrix.com

Microarrays traditionally have been used to analyze the expression behavior of large numbers of coding transcripts. Here we present a comprehensive approach for high-throughput transcript discovery in Escherichia coli focused mainly on intergenic regions which, together with analysis of coding transcripts, provides us with a more complete insight into the organism’s transcriptome. Using a whole genome array, we detected expression for 4052 coding transcripts and identified 1102 additional transcripts in the intergenic regions of the E.coli genome. Further classification reveals 317 novel transcripts with unknown function. Our results show that, despite sophisticated approaches to genome annotation, many cellular transcripts remain unidentified. Through the experimental identification of all RNAs expressed under a specific condition, we gain a more thorough understanding of all cellular processes.


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