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Series GSE39804 Query DataSets for GSE39804
Status Public on Aug 01, 2012
Title Inference of pathways, non-coding RNAs and regulatory elements during iron deprivation of Synechocystis based on comprehensive expression profiling
Organism Synechocystis sp. PCC 6803
Experiment type Expression profiling by array
Summary Iron is an essential cofactor in many metabolic reactions. Mechanisms controlling iron homeostasis need to respond to changes in extracellular conditions, but must also keep the concentration of intracellular iron under strict control, as free ferrous iron (Fe2+) can lead to the generation of reactive oxygen species. Due to its role as redox carrier in photosynthesis, the iron quota in cyanobacteria is about 10 times higher than in model enterobacteria, but the molecular details how such high quota is tightly regulated have remained obscure. Here, we measured time-resolved gene expression changes after iron depletion in the cyanobacterium Synechocystis sp. PCC 6803 using a comprehensive microarray platform monitoring both protein-coding and non-coding transcripts. In total, 644 protein-coding genes were differentially expressed during the first 72h. Many of these proteins are associated with iron transport, photosynthesis or ATP synthesis. Comparing our data with three previous studies, we identified a core set of 28 genes involved in the iron stress response. Among them were genes encoding proteins important for assimilation of inorganic carbon, suggesting a previously unknown link between the carbon and iron regulatory networks. Nine of the 28 genes are of unknown function and constitute key targets for detailed functional analysis. Applying identical statistical and clustering criteria as for the protein-coding fraction, we also identified 10 small RNAs, 62 anti-sense RNAs, four 5’UTRs and 7 intergenic elements as likely to be involved in the iron regulatory network. Hence, our genome-wide profiling results indicate an unprecedented complexity in the iron-related regulatory network of cyanobacteria.
Overall design We monitored iron limitation stress induced gene expression changes in the cyanobacterial model organism Synechocystis sp. PCC 6803. We included a control sample without iron-stress (0h) and 5 samples from timepoints after stress induction (3h, 12h, 24h, 48h, 72h). Each timepoint was sampled from two independent biological replicates.
Contributor(s) Hernández-Prieto MA, Schön V, Georg J, Barreira L, Varela J, Hess WR, Futschik ME
Citation(s) 23275872
Submission date Aug 01, 2012
Last update date Jan 23, 2017
Contact name Jens Georg
Organization name University of Freiburg
Street address Schänzlestr. 1
City Freiburg
ZIP/Postal code 79104
Country Germany
Platforms (1)
GPL15867 Agilent-027432 Syn6803_expressions454_4-3probes
Samples (12)
GSM979518 Synechocystis PCC6803, 0h, rep1
GSM979519 Synechocystis PCC6803, 0h, rep2
GSM979520 Synechocystis PCC6803, 3h, rep1
BioProject PRJNA171743

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39804_RAW.tar 73.7 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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