GEO DataSets

(Submitter supplied) Investigation of gene expression changes in a DvH genotype ES10-5, a strain isolated from population ES10 which has been evolved under salt stress for 5000 generations. The gene expression was compared to a gentype ES9-11 isolated from ES9 evolved under the same condition for 1200 generations and the ancestral strain. The genotype ES10-5 was characterized in this study. ES9-11 was isolated and characterized in Zhou A et al., 2013. more...

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL24011

18 Samples

Download data: FTR, TXT

(Submitter supplied) Managing tradeoffs through gene regulation is believed to maintain resilience of a microbial community in a fluctuating resource environment. To investigate this hypothesis we imposed a fluctuating environment that required the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. more...

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21574

29 Samples

Download data: TXT

(Submitter supplied) Managing tradeoffs through gene regulation is believed to be critical for the success of a generalist in a fluctuating resource environment. To investigate this hypothesis in depth, we imposed a fluctuating environment that required a representative community of the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. more...

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL20930

24 Samples

Download data: TXT

(Submitter supplied) Differental gene expression of three consortia: Dhc195/DVH with exogenous cobalamin, Dhc195/DVH/PF with exogenous cobalamin, Dhc195/DVH/PF without exogenous cobalamin Acronyms: Dhc195: Dehalococcoides mccartyi strain 195; DVH: Desulfovibrio vulgaris Hildenborough; PF: Pelosinus fermentans strain R7

Organism:

Dehalococcoides mccartyi VS; Nitratidesulfovibrio vulgaris str. Hildenborough; Dehalococcoides mccartyi CBDB1; Pelosinus fermentans DSM 17108; Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi 195

Type:

Expression profiling by array

Platform:

GPL10838

9 Samples

Download data: CEL

(Submitter supplied) Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains. gene expression changes in evolved salt-stressed DvH strain (ES, evolved in LS4D + 100 mM NaCl for 1200 generations), evolved control DvH strain (EC, evolved in LS4D for 1200 generations) and ancestor DvH strain grown in non-stress (LS4D), low salt stress (LS4D + 100 mM NaCl) or high salt stress (LS4D + 250 mM NaCl) conditions

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

9 Samples

Download data: TXT

(Submitter supplied) Investigating the role of carbon monoxide and a CO sensor protein CooA in the physiology of Desulfovibrio vulgaris Hildenborough using whole genome expression analysis

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL15376

3 Samples

Download data: TXT

(Submitter supplied) Background. Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. more...

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

2 Samples

Download data: TXT

(Submitter supplied) Using gene expression changes at mid-log phase data from microarray experiments, we investigated the roles of global transcription regulators in D. vulgaris.

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

5 Samples

Download data: TXT

(Submitter supplied) Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris. Keywords: stress response, time course

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

16 Samples

Download data: TXT

(Submitter supplied) Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris. Keywords: stress response, time course

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

16 Samples

Download data: TXT

(Submitter supplied) The syntrophic growth of strain 195 with Desulfovibrio vulgaris Hildenborough (DVH) and/or Methanobacterium congolense (MC) enhanced TCE dechlorination process by faster dechlorination rate and more robust growth. Transcriptomes of strain 195 grown in isolation, co- and tri-cultures were obtained by microarray experiments to find out the differential expressed genes corresponding to the syntrophic growth. more...

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough; Methanobacterium congolense; Dehalococcoides mccartyi 195

Type:

Expression profiling by array

Platform:

GPL6116

12 Samples

Download data: CEL

(Submitter supplied) Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris. Keywords: stress response, time course

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

12 Samples

Download data: TXT

(Submitter supplied) Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris. Keywords: stress response, time course

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

16 Samples

Download data: TXT

(Submitter supplied) D. vulgaris is a model sulfate reducing bacteria whose genome encodes a high number of two component systems, including 29 DNA-binding response regulators (RRs) whose functions are unknown, but are very likley to be important to the environmental lifestyle of the organism. We determined the gene targets for 24 of these RRs using purified His-tagged RR and sheared genomic DNA in an in vitro DAP-chip (DNA-affinity-purified - chip) assay. more...

Organism:

Nitratidesulfovibrio vulgaris; Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL11167

34 Samples

Download data: PAIR

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

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL13656 GPL13654

4 Samples

Download data: FTR, WIG

(Submitter supplied) 5' RNASeq of mRNA from DvH in defined lactate/sulfate media (LS4D)

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13656

2 Samples

Download data: WIG

(Submitter supplied) High-resolution tiling analysis of the DvH transcriptome in lactate/sulfate media, both rich (LS) and defined (LS4D)

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by genome tiling array

Platform:

GPL13654

2 Samples

Download data: FTR

(Submitter supplied) Using data from microarray experiments, we investigated the effects of excess sodium nitrate on D. vulgaris. Keywords: stress response, time course

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL5214

9 Samples

Download data: TXT

(Submitter supplied) Differences in gene expression between a mutant D. vulgaris strain missing the PerR transcriptional regulator gene and the wild-type strain.

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL6459

2 Samples

Download data: TXT

(Submitter supplied) This set of microarray data was used to compare the effects of D. vulgaris grown syntrophically with a hydrogenotrophic methanogen versus D. vulgaris grown in sulfate-limited monoculture. Keywords: physiological response, one time point (stable continuous culture for both control and treated cells)

Organism:

Nitratidesulfovibrio vulgaris str. Hildenborough

Type:

Expression profiling by array

Platform:

GPL9107

1 Sample

Download data: TXT