E-GEOD-56502 - Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

Status
Released on 5 April 2014, last updated on 8 April 2014
Organism
Burkholderia thailandensis E264
Samples (162)
Array (1)
Protocols (5)
Description
Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology. We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions (IGRs) greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors. 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.
Experiment type
transcription profiling by array 
Contacts
Chris J Stubben <geo@ncbi.nlm.nih.gov>, Elizabeth Hong-Geller, John M Dunbar, Sarah K Buddenborg, Sofiya N Micheva-Viteva, Yulin Shou
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-56502.idf.txt
Sample and data relationshipE-GEOD-56502.sdrf.txt
Raw data (1)E-GEOD-56502.raw.1.zip
Processed data (1)E-GEOD-56502.processed.1.zip
Array designA-GEOD-18529.adf.txt
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