Unknown,Transcriptomics,Genomics,Proteomics

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


ABSTRACT: 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

ORGANISM(S): Escherichia coli

SUBMITTER: Jinseong Cheong 

PROVIDER: E-GEOD-1121 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Integrating high-throughput and computational data elucidates bacterial networks.

Covert Markus W MW   Knight Eric M EM   Reed Jennifer L JL   Herrgard Markus J MJ   Palsson Bernhard O BO  

Nature 20040501 6987


The flood of high-throughput biological data has led to the expectation that computational (or in silico) models can be used to direct biological discovery, enabling biologists to reconcile heterogeneous data types, find inconsistencies and systematically generate hypotheses. Such a process is fundamentally iterative, where each iteration involves making model predictions, obtaining experimental data, reconciling the predicted outcomes with experimental ones, and using discrepancies to update th  ...[more]

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