Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 162
Release date: Apr 5 2014
Last update date: Jul 13 2014
Access: Public
Dataset link Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

Experimental Protocol


A custom Affymetrix microarray was designed using Burkholderia thailandensis E264 gene annotations from Pathema and included 8711 probe sets targeting 5557 protein-coding genes and 2908 IGRs longer than 90 bases on the plus strand. Experiments were performed in four classes of media: nutrient broth, M9-minimal media, Luria broth, and various host conditions such as brain-heart infusion, calf serum, or tryptic soy broth. There were 101 samples in four time course arrays measuring temperature increase, pH drop, salt stress, and phosphate starvation (21 distinct conditions). Each condition was grown at 37° C, except the initial temperature experiment at 25°C, and replicated five times. In order to survey a diverse range of environmental and stress conditions, another 10 replicated and 23 unreplicated treatments were also tested.

Repositories


GEO

GSE56502

ArrayExpress

E-GEOD-56502

BioProject

PRJNA243618

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