Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 90
Release date: Apr 6 2016
Last update date: Apr 7 2016
Access: Public
Chemicals: Guanine, Nucleotides, Purines, Hypoxanthine
Dataset link Transcriptome analysis of Escherichia coli during dGTP Starvation

Experimental Protocol


The present study was aimed at understanding the metabolic changes in dGTP-starved cells. To do so, we designed two experiments. The first experiment was aimed at investigating the transcriptional consequences of loss of the Hx purine source in each of the four strains (wt, optA1, gpt, and optA1 gpt). Here, hypoxanthine was withdrawn from actively growing cells starting at OD 0.1, and periodic 2-fold dilutions were applied to keep to OD of the growing cultures below or only slightly above 0.20 (low-dilution protocol). Samples were taken for microarray analysis at 15, 30, 45, 60, and 120 min. At each time point RNA samples were taken and analyzed for gene expression changes using the Affymetrix GeneChip E. coli Genome 2.0 Array. This experiment was conducted three times, independently. A second experiment was aimed at following the transcriptional changes in the optA1 gpt strain during the entire 6-hour time course including the filamentation and cell death stage. Here, we used a slightly different dilution protocol (high-dilution protocol), in which the strain was initially highly diluted (OD630 = 0.01) and further diluted at strategic points to prevent the OD to rise above 0.1. These conditions optimize the cell death phenomenon. This experiment was also conducted three times independently.

Repositories


GEO

GSE80002

ArrayExpress

E-GEOD-80002

BioProject

PRJNA317595

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Contact


NIEHS Microarray Core