GEO DataSets

(Submitter supplied) In this work we analyzed changes in gene espression in Shewanella baltica upon cold stress. In order to imitate natural environment, we cultured bacteria in the Instant Ocean medium in a chemostat. Samples were collected after 90 and 180 minutes of cold stress and analyzed by RNA sequencing. The transcriptomic response could be characterized as global downregulation of gene expression (613 genes downregulated) and we found only 242 genes which were upregulated. more...

Organism:

Shewanella baltica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28560

5 Samples

Download data: TXT, WIG

(Submitter supplied) Transcriptional profiling of Shewanella OS185 and OS195 strains grown under aerobic, anaerobic thiosulfate and nitrate respiratory conditions.

Organism:

Shewanella baltica

Type:

Expression profiling by array

Platform:

GPL23607

18 Samples

Download data: GPR

(Submitter supplied) Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a salinity up-shift. R. baltica cultures were grown at 28°C in mineral media with 17.5% salinity and up-shifted to 59.9%. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift.

Organism:

Rhodopirellula baltica SH 1; Rhodopirellula baltica

Type:

Expression profiling by array

Platform:

GPL7654

18 Samples

Download data: TXT

(Submitter supplied) Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a temperature up-shift. R. baltica cultures were grown at 28°C and then shifted to 6°C. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift (28°C).

Organism:

Rhodopirellula baltica; Rhodopirellula baltica SH 1

Type:

Expression profiling by array

Platform:

GPL7654

18 Samples

Download data: TXT

(Submitter supplied) Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a temperature up-shift. R. baltica cultures were grown at 28°C and then shifted to 37°C. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift (28°C). Time series experiment, whole genome array

Organism:

Rhodopirellula baltica; Rhodopirellula baltica SH 1

Type:

Expression profiling by array

Platform:

GPL7654

18 Samples

Download data: TXT

(Submitter supplied) CGH of 46 Shewanella baltica strains using customized oligonucleotide microarrays

Organism:

Shewanella baltica

Type:

Genome variation profiling by array

Platform:

GPL23607

46 Samples

Download data: GPR, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by array

Platform:

GPL16568

12 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by array

Platform:

GPL16568

18 Samples

Download data

(Submitter supplied) Arctic Mesorhizobium strain N33 was isolated from nodules of the Oxytropis arctobia in Canada’s eastern Arctic. This symbiotic bacterium can grow from 0 to 30°C, is one of the best known cold-adapted rhizobia, and can fix nitrogen at ~10°C. Here, the key molecular mechanisms of cold adaptation were investigated by determining changes in transcript profiles when cells were treated under eight different temperature conditions, including both sustained and transient cold treatments compared with cells grown at room temperature.

Organism:

Mesorhizobium sp. N33

Type:

Expression profiling by array

Platform:

GPL19113

42 Samples

Download data: GPR

(Submitter supplied) This study presents a global transcriptional analysis of the cold shock response of Shewanella oneidensis MR-1 after a temperature downshift from 30 to 8 or 15oC based on time-series microarray experiments. More than 700 genes were found to be significantly affected (p < 0.05) upon cold shock challenge, especially at 8oC. The temporal gene expression patterns of the classical cold-shock genes varied and only some of them, most notably so1648 and so2787, were differentially regulated in response to temperature downshift. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL3253

60 Samples

Download data

(Submitter supplied) In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA-Seq analysis was employed to determine differential gene expression over time from cultures maintained in a chemostat and limited for oxygen. more...

Organism:

Shewanella oneidensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21696

16 Samples

Download data: TXT

(Submitter supplied) To investigate low-temperature tolerance of the bacterium, three in-frame gene deletion mutants of VpacspA and VpacspD were constructed using homologous recombination method. When compared to the wild type strain, the growth of ΔVpacspA mutant was strongly repressed at 10 0C, whereas the deletion of VpacspD gene greatly activated the bacterium growth at the low temperature. Transcriptome data revealed that 12.4% of the expressed genes in V. more...

Organism:

Vibrio parahaemolyticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19796

4 Samples

Download data: TXT

(Submitter supplied) The microarray experiment compare the transcriptome of PV-4 wild type versus the deltahemH1 mutant, a PPIX accumulating strain. Only part of the data is used in the manuscript and we are working on this dataset for future manuscripts

Organism:

Shewanella loihica PV-4

Type:

Expression profiling by array

Platform:

GPL21934

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by array

Platform:

GPL16568

18 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by array

Platform:

GPL16568

12 Samples

Download data

(Submitter supplied) The hns gene was deleted from WP3 genome to construct the WP3Δhns strain. The two strains were cultured at 20°C and the transcriptional profiles were compared.

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by array

Platform:

GPL16568

6 Samples

Download data: LSR

(Submitter supplied) The hns gene was deleted from WP3 genome to construct the WP3Δhns strain. The two strains were cultured at 4°C and the transcriptional profiles were compared.

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by array

Platform:

GPL16568

6 Samples

Download data: LSR

(Submitter supplied) Temperature is a crucial environmental signal that govers the occurrence of Vibrio cholerae and cholera outbreaks. To understand how temperature impacts the transcriptome of V. cholerae we performed whole-genome level transcriptional profiling using custom microarrays on cells grown at human body temperature (37 C) then shifted to temperatures V. cholerae experience in the environment (15 C and 25 C).

Organism:

Vibrio cholerae

Type:

Expression profiling by array

Platform:

GPL20916

18 Samples

Download data: GPR

(Submitter supplied) The prophage and RF DNA of SW1 were removed from WP3 to construct the phage-free strain. The two strains were cultured at 4°C and the transcriptional profiles were compared.

Organism:

Shewanella piezotolerans WP3

Type:

Expression profiling by array

Platform:

GPL16568

2 Samples

Download data: LSR

(Submitter supplied) The sumitted data compares gene expression profile of Shewnaella oneidensis MR-1 on two different sets of media conditions (nutritionally rich LB medium and Lactate minimal medium)

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL8434

84 Samples

Download data: CEL