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Synechocystis PCC6803 time course responses to cadmium (CdSO4, 50 microM, 300 min.

ABSTRACT: The transcriptome approach was used to characterize the of the global change in Synechocystis gene expression in response to continuous exposure to cadmium (50 microM). Total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: stress responses

ORGANISM(S): Synechocystis sp. PCC 6803

PROVIDER: GSE3718 | GEO | 2005/12/07

SECONDARY ACCESSION(S): PRJNA94301

REPOSITORIES: GEO

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Synechocystis PCC6803 time course responses to zinc (ZnSO4, 776 microM.

Project description:The transcriptome approach was used to characterize the of the global change (2 time points) in Synechocystis gene expression in response to continuous exposure to zinc excess (776 microM), compared to standard medium (776 nM). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: stress responses

2005-12-07 | GSE3716 | GEO

Synechocystis PCC6803 time course responses to iron (ferric ammonium citrate, 17 mM.

Project description:The transcriptome approach was used to characterize of the global change (2 time points) in Synechocystis gene expression in response to continuous exposure to iron excess (17 mM), compared to standard medium (17 microM). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: stress responses

2005-12-07 | GSE3715 | GEO

knock-out Slr1738 mutant strain analysis exposed to cadmium (50 microM).

Project description:The transcriptome approach was used to characterize the global change in slr1738 null-mutant gene expression in response to cadmium (50 microM, 180 min), compared to wild type strain gene expression in response to cadmium (50 microM, 180 min). Total RNA were isolated from null-mutant and wild type stressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: stress responses

2005-12-07 | GSE3719 | GEO

Synechocystis PCC6803 dose responses to iron starvation (96h).

Project description:The transcriptome approach was used to characterize the global change (2 Fe concentrations) in Synechocystis gene expression in response to continuous iron starvation, compared to standard medium (17 microM). For iron depletion, exponentially growing cells were washed in Fe-free medium, and grown for 48 hrs under standard conditions in liquid medium cotaining either 1 mM or 2 mM of ferric ammonium citrate. Then, cells were washed, and resuspended in Fe-free medium (Fe contaminations 0.5 microM) and grown for another 48 hrs period. For each concentration point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each concentration point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: stress responses

2005-12-07 | GSE3717 | GEO

Synechocystis PCC6803 time course responses to H2O2 3mM.

Project description:The transcriptome approach was used to characterize the kinetics (5 time points) of the global change in Synechocystis gene expression in response to continuous exposure to H2O2 (3 mM). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: time course, stress responses

2005-12-07 | GSE3703 | GEO

Synechocystis PCC6803 time course responses to 50 µM cadmium

Project description:The transcriptome approach was used to characterize the kinetics (9 time points) of the global change in Synechocystis gene expression in response to continuous exposure to Cd (CdSO4, 50 _M). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point), covering 2,845 of the 3,168 ORFs of Synechocystis (Custom-commercial array : IntelliGeneTM CyanoCHIP version 1.2, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: time course, stress responses

2005-12-01 | GSE3682 | GEO

Time course response of Synechocystis PCC 6803 to dehydration/desiccation

Project description:The responses of the transcriptome were monitored in Synechocysis PCC 6803 during a linear rate of evaporation of the culture to dryness (desiccation). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: Dehydration, stress response, time course, transcription, cyanobacteria

2006-09-04 | GSE4604 | GEO

Time course response of Synechocystis PCC 6803 to UV irradiation

Project description:The responses of the transcriptome of Synechocystis PCC 6803 to UV-irradiation were measured at time points over 36 h. Irradiation was provided by Sylvania soft white DuluzR compact fluorescent 23W bulbs (Osram Sylvania Ltd, Mississauga, Canada), a 20W RS UV-B medical light with a spectral maximum at 310 nm (model ‘TL’, Philips, Holland), and 15W black lights each with a spectral maximum at 368 nm (model F15T8-BL, General Electric, USA). Total quantum scalar irradiance was measured with a model QSL-100 meter (Biospherical Instruments Inc., San Diego, CA). The flux densities of the UV-A and UV-B components of the spectrum were measured with DIX series UV-B and 365A sensors, respectively, with a Spectroline DRC-100X digital radiometer (Spectronics Corporation, Westbury, NY). In these experiments full illumination represented a continuous photon flux density in the visible range of 330 μmol photons m-2 s-1, with UV-A and UV-B maxima of 3.8 x 10^6 and 0.8 x 10^6 mW m-2, respectively. All values reported were the incident fluxes within culture vessels at the immediate surface of the cell suspensions. Aliquot cultures (in duplicate) were harvested after 0, 15 min, 1 h, 3 h, 6 h, 12 h, 24 h and 36 h of UV-irradiation. For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: UV-irradiation, desiccation, Synechocystis PCC 6803, cyanobacteria, time course, transcription

2006-09-04 | GSE4606 | GEO

Formaldehyde stress response in Methylobacterium extorquens AM1

Project description:The goal of this study was to use microarrays to identify genes differentially regulated under conditions of formaldehyde stress relative to two other stress conditions (oxidative, osmotic) in an effort to identify genes that might be involved in a formaldehyde-specific stress response, rather than a general stress response, in the model methylotroph Methylobacterium extorquens AM1. Two color experiment, three treatments, three biological replicates per treatment, and two technical (dye swap) replicates per biological replicate: formaldehyde-stressed vs. unstressed cells; oxidative-stressed vs. unstressed cells; and osmotic-stressed vs. unstressed cells.

2015-01-01 | E-GEOD-15631 | biostudies-arrayexpress

Posttranscriptional mRNA expression changes in stress

Project description:HEK T293 cells were treated with Anisomycin or the solvent control DMSO. Cells were fractionated and cytoplasmic and nuclear RNA were isolated. pre-mRNA-Seq was performed on stressed and unstressed nuclear RNA samples. mRNA-Seq was performed on stressed and unstressed cytoplasmic RNA samples. In addition, polyadenylation sites were globally mapped by applying the 3'T-fill method on the same stressed and unstressed cytoplasmic RNA samples.

2016-07-13 | E-MTAB-3585 | biostudies-arrayexpress

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