E-GEOD-1121 - Transcription profiling of E. coli mutant and wild type cultures grown under aerobic or anaerobic conditions

Status
Submitted on 9 March 2004, released on 22 July 2007, last updated on 27 March 2012
Organism
Escherichia coli
Samples (43)
Array (1)
Protocols (2)
Description
The purpose of this study is to investigate the changes of global gene expression in E. coli during an oxygen shift. All cultures were grown under aerobic or anaerobic conditions in M9 minimal media supplemented with glucose. Samples were RNA-stabilized using Qiagen RNAProtect Bacterial Reagent, and total RNA was isolated from exponentially growing cells using a Qiagen RNeasy mini kit (protocols available at www1.qiagen.com). The RNA (10 µg) was then used as the template for cDNA synthesis, the product of which was fragmented, labelled, and hybridized to an Affymetrix E. coli Antisense Genome Array, which was washed and scanned to obtain an image. All of these steps were performed according to Affymetrix protocols (available at www.affymetrix.com). This SuperSeries is composed of the following subset Series:; GSE1106: aerobic knock-out; GSE1107: anaerobic knock-out Experiment Overall Design: Refer to individual Series
Experiment types
transcription profiling by array, co-expression, growth condition, individual genetic characteristics
Contact
Citation
Integrating high-throughput and computational data elucidates bacterial networks. Markus W Covert, Eric M Knight, Jennifer L Reed, Markus J Herrgard, Bernhard O Palsson. Nature 429(6987):92-6 (2004)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-1121.idf.txt
Sample and data relationshipE-GEOD-1121.sdrf.txt
Raw data (1)E-GEOD-1121.raw.1.zip
Processed data (1)E-GEOD-1121.processed.1.zip
Array designA-AFFY-29.adf.txt
R ExpressionSetE-GEOD-1121.eSet.r
Links