GEO DataSets

(Submitter supplied) Vibrio vulnificus (V. vulnificus) is an opportunistic human pathogen known for causing various illnesses such as gastroenteritis, skin and muscle necrosis, septic shock, and sepsis. This halophilic estuarine bacterium's growth and infection process involves adaptation to both the natural briny environments and the host. OmpR, a response regulator in the EnvZ/OmpR two-component regulatory system (TCS), is crucial for environmental adaptation and pathogenicity. more...

Organism:

Vibrio vulnificus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35086

6 Samples

Download data: TXT

(Submitter supplied) We show that DANCE-MaP permits measurement of state-specific per-nucleotide reactivities, direct secondary structure PAIRs, and tertiary RINGs for RNA structural ensembles. Here, we demonstrate DANCE-MaP on the V. vulnificus add riboswitch.

Organism:

Vibrio vulnificus

Type:

Other

Platform:

GPL27000

32 Samples

Download data: TAR

(Submitter supplied) The goal of this set of experiments is to determine the structure of HIV-1 NL4-3 and NHG RNA structure using a novel algorithm that allows for the identification of multiple RNA folding conformations. The input data used for this algorithm is DMS-MaPseq data. We focused on two specific areas of the HIV-1 genome, the Rev Response Element (RRE) and A3 splice acceptor site, as well as probing the whole HIV-1 genome. more...

Organism:

Homo sapiens; synthetic construct; Human immunodeficiency virus 1; Vibrio vulnificus

Type:

Other

7 related Platforms

23 Samples

Download data: TXT

(Submitter supplied) Structure probing experiments were performed on in vitro transcripts and E. coli and human cell cultures under natively extracted (cell-free) and in-cell conditions to benchmark the performance of the newly introduced PAIR-MaP correlated chemical probing strategy for detecting RNA duplexes. Multiple-hit dimethyl sulfate (DMS) probing was done using new buffer conditions that facilitate DMS modification of all four nucleotides.

Organism:

Vibrio vulnificus; Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL16085 GPL27000 GPL15520

23 Samples

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(Submitter supplied) Small octopus is one of the major source for V. vulnificus outbreak among aquatic products in Northeast Asian due to improperly cooking and wound infection by mishandling. However, there is no report on whole genome sequence of V. vulnificus isolated from contaminated surf clam, thus no information is available for major virulence factors about V. vulnificus obtained from small octopus. Therefore, the analysis of transcriptome of isolated V. more...

Organism:

Vibrio vulnificus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23679

8 Samples

Download data: TXT

(Submitter supplied) VarS/A is one of the global factors regulating diverse aspects of metabolism and virulence of bacteria including pathogenic Vibrio spp. An experiment to identify VarS/A-regulon in V. vulnificus revealed that a putative LuxR-type transcriptional regulator was down-regulated in ΔvarA mutant. To investigate the roles of this regulatory cascade from VarS/A to a LuxR-type regulator in V. vulnificus, the target gene regulated by a LuxR-regulator was identified and its expression was characterized.

Organism:

Vibrio vulnificus; Vibrio vulnificus MO6-24/O

Type:

Expression profiling by array

Platform:

GPL19927

9 Samples

Download data: GPR

(Submitter supplied) V. vulnificus is a marine bacteria that causes diseases in both mammals and fish. In both hosts, the iron concentration represents a key factor that greatly influences the virulence of this bacterium. To further define the gene repertoire that is regulated by iron concentration and Fur protein (the main transcriptional regulator in response to iron concentration) in V. vulnificus, we obtained a mutant in Fur and used DNA microarray technology to monitor the expression of the entire gene repertoire in response to iron. more...

Organism:

Vibrio vulnificus

Type:

Expression profiling by array

Platform:

GPL19040

12 Samples

Download data: TXT

(Submitter supplied) The profiles of transcripts from the planktonic cells and biofilm cells of V. vulnificus were compared by using a V. vulnificus whole-genome microarray

Organism:

Vibrio vulnificus; Vibrio vulnificus CMCP6

Type:

Expression profiling by array

Platform:

GPL17798

6 Samples

Download data: TXT

(Submitter supplied) Two-condition experiment, Wild-type biofilm cells vs. smcR mutant biofilm cells. Biological replicates: 3 control, 3 mutant strains, independently grown and harvested. One replicate per array. A significant portion of the SmcR regulon predicted on the basis of microarray analysis results is indeed regulated by SmcR and that SmcR functions on biofilm dispersion in V. vulnificus.

Organism:

Vibrio vulnificus

Type:

Expression profiling by array

Platform:

GPL14598

3 Samples

Download data: GPR, TXT

(Submitter supplied) Two-condition experiment, Wild-type vs. smcR mutant. Biological replicates: 3 control, 3 mutant strains, independently grown and harvested. One replicate per array. A significant portion of the SmcR regulon predicted on the basis of microarray analysis results is indeed regulated by SmcR and that SmcR is a global regulator in V. vulnificus.

Organism:

Vibrio vulnificus

Type:

Expression profiling by array

Platform:

GPL14588

6 Samples

Download data: GPR

(Submitter supplied) Agilent Vvulnificus SS microarray V2.0 Protocol: see manufacturer's web site at http://www.agilent.com/

Organism:

Vibrio vulnificus

1 Series

12 Samples

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(Submitter supplied) See manufacturer's web site at http://www.agilent.com/

Organism:

Vibrio vulnificus

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(Submitter supplied) The V. vulnificus whole genome TwinChip, which has two blocks, up (upper) and dn (lower), manufactured by e-biogen (Seoul, South Korea). The slide contains 3 arrays of 15,000 features each. One array consists of a grid of 160 columns by 94 rows for a total of 15,040 spots with 40 spots reserved for internal quality control, leaving 15,000 spots available for custom probe sequences. This format is compatible with the four-chamber Agilent Technologies hybridization gasket slide.

Organism:

Vibrio vulnificus

1 Series

3 Samples

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(Submitter supplied) The V. vulnificus whole genome TwinChip, which has two blocks, up (upper) and dn (lower), manufactured and kindly provided by the 21C Frontier Microbial Genomics and Applications Center (Daejeon, South Korea)

Organism:

Vibrio vulnificus

1 Series

6 Samples

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(Submitter supplied) This set includes 10210 oligonucleotides, has 23232 spots distributed in 48 blocks. Protocol: QVV, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000

Organism:

Vibrio vulnificus

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(Submitter supplied) This set includes 10210 oligonucleotides, has 23232 spots distributed in 48 blocks. Protocol: QVV, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000

Organism:

Vibrio vulnificus

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(Submitter supplied) The PCR products were purified using Qiagen PCR purification kit, and printed on Corning GAPS II coated slide in quadriplicate using a DNA arrayer, Affimatrix 427. This set includes 160 genes, DNA fragment spanning about a 700-bp region of the 3¡Çend portion of each gene was prepared by PCR using primers specific to DNA nucleotide sequence of each gene designed based on the genome sequences of V. vulnificus in the GenBank (Accession numbers NC_004459 and NC_004460) Keywords = Vibrio vulnificus, cyclic dipeptide

Organism:

Vibrio vulnificus

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