Vibrio cholerae vpsT microarray analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Vibrio cholerae
PROVIDER: GSE19479 | GEO | 2010/04/01
SECONDARY ACCESSION(S): PRJNA122269
REPOSITORIES: GEO
Similar Datasets
Project description:A1552tfoX/pBAD and A1552tfoX/pBAD-tfoX were diluted 1:100 from over night cultures and grown in LB liquid medium containing 0.2 % L-arabinose and 100 μg/ml ampicillin. At OD600=0.3, samples were quickly harvested in a microcentrifuge at room temperature and the bacterial pellet resuspended in Trizol reagent (GIBCO/BRL) and kept at -80:C. The aqueous phase containing the RNA was isolated according to the manufacturers manual and to which was added an equal volume of 70% ethanol. Using an RNeasy. column (Qiagen, Valencia, CA) the RNA was isolated and treated with DNase I solution. Labeling of cDNA was done as described by M. I. Voskuil et al., J. Exp. Med. 198, 705-13 (2003). Samples from A1552tfoX/pBAD were labeled with Cy3 and samples from A1552tfoX/pBAD-tfoX were labeled with Cy5. Duplicate samples from two individual experiments were hybridized to an oligonucleotide DNA microarray slide containing at least one oligonucleotide corresponding to every identified open-reading-frame of V. cholerae O1 El Tor strain N16961. Microarray slides were prehybridized (5 x SSC, 1% BSA, 0.1% SDS) for at least one hour at 42:C and hybridization was performed in 2 x SSC, 0.1% SDS, 20% formamide at 54:C over night.
2006-11-08 | E-SMDB-3535 | biostudies-arrayexpress
Project description:This study is an analysis of changes in gene expression during stringent response in Vibrio cholerae. V. cholerae cells in mid-log were treated with serine hydroxamate and gene expression was compared to untreated cells. Keywords: Stress response, stringent response
2006-12-28 | GSE6616 | GEO
Project description:Question Addressed: Does gene expression in V. cholerae change when samples are frozen at -80 degrees? An in vitro grown culture of O1 Inaba ICDDR,B (strain DSM-V999 described in Nature. 2002 Jun 6;417(6889):642-5) that had been grown to exponential phase (OD600 + 0.2) was placed in a 15 ml conical and then placed in a -80 degree freezer. A portion of the starting culture was harvested prior to freezing to serve as the control/reference for downstream hybridizations. RNA was recovered from the non-frozen sample as well as by prepping material directly from frozen samples. Labeling reactions were performed in quadruplicate for each sample. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
2013-05-23 | GSE38179 | GEO
Project description:Each sample was infected with a different strain of V. Cholerae Keywords = Cholerae Keywords: parallel sample
2004-10-14 | GSE1549 | GEO
Project description:Transcriptional profiling comparing a V. cholerae cpxA* mutant relative to WT at an OD600 of 1.
2014-05-03 | GSE55037 | GEO
Project description:Abstract: Chitin, an insoluble polymer of GlcNAc, is an abundant source of carbon, nitrogen, and energy for marine microorganisms. Microarray expression profiling and mutational studies of Vibrio cholerae growing on a natural chitin surface, or with the soluble chitin oligosaccharides (GlcNAc)(2-6), GlcNAc, or the glucosamine dimer (GlcN)2 identified three sets of differentially regulated genes. We show that (i) ChiS, a sensor histidine kinase, regulates expression of the (GlcNAc)(2-6) gene set, including a (GlcNAc)2 catabolic operon, two extracellular chitinases, a chitoporin, and a PilA-containing type IV pilus, designated ChiRP (chitin-regulated pilus) that confers a significant growth advantage to V. cholerae on a chitin surface; (ii) GlcNAc causes the coordinate expression of genes involved with chitin chemotaxis and adherence and with the transport and assimilation of GlcNAc; (iii) (GlcN)2 induces genes required for the transport and catabolism of nonacetylated chitin residues; and (iv) the constitutively expressed MSHA pilus facilitates adhesion to the chitin surface independent of surface chemistry. Collectively, these results provide a global portrait of a complex, multistage V. cholerae program for the efficient utilization of chitin. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4388 | GEO
Project description: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).
2016-05-09 | GSE81158 | GEO
Project description:Vibrio cholerae strains A1552tfoX/pBAD and A1552tfoX/pBAD-tfoX were diluted 1:100 from over night cultures and grown in LB liquid medium containing 0.2 % L-arabinose and 100 μg/ml ampicillin. At OD600=0.3, samples were quickly harvested in a microcentrifuge at room temperature and the bacterial pellet resuspended in Trizol reagent (GIBCO/BRL) and kept at -80 degrees C. The aqueous phase containing the RNA was isolated according to the manufacturer's manual and to which was added an equal volume of 70% ethanol. Using an RNeasy. column (Qiagen, Valencia, CA) the RNA was isolated and treated with DNase I solution. Labeling of cDNA was done as described by M. I. Voskuil et al., J. Exp. Med. 198, 705-13 (2003). Samples from A1552tfoX/pBAD were labeled with Cy3 and samples from A1552tfoX/pBAD-tfoX were labeled with Cy5. Duplicate samples from two individual experiments were hybridized to an oligonucleotide DNA microarray slide containing at least one oligonucleotide corresponding to every identified open-reading-frame of V. cholerae O1 El Tor strain N16961. Microarray slides were prehybridized (5 x SSC, 1% BSA, 0.1% SDS) for at least one hour at 42 degrees C and hybridization was performed in 2 x SSC, 0.1% SDS, 20% formamide at 54 degrees C over night. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-12-15 | GSE3577 | GEO
Project description:Question Addressed: What is the level of expression of genes in Vibrio cholerae recovered from various conditions. These conditions include samples recovered directly from patients (O139 from stool samples from ICDDR,B and N16961 from stool samples from a vaccine trial held in Cincinnati) as well as standard logarithmic and stationary phase grown bacteria. Labeling reactions were performed in duplicate for each stool derived and in quadruplicate for each in vitro grown strain. A common reference was used for each slide, it was composed of RNA from the exponentially growing 92A1552 V. cholerae strain
2013-05-23 | GSE38178 | GEO
Project description:Question Addressed: Does gene expression in V. cholerae change when samples are frozen at -80 degrees? An in vitro grown culture of O1 Inaba ICDDR,B (strain DSM-V999 described in Nature. 2002 Jun 6;417(6889):642-5) that had been grown to exponential phase (OD600 + 0.2) was placed in a 15 ml conical and then placed in a -80 degree freezer. A portion of the starting culture was harvested prior to freezing to serve as the control/reference for downstream hybridizations. RNA was recovered from the non-frozen sample as well as by prepping material directly from frozen samples. Labeling reactions were performed in quadruplicate for each sample. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. replicate_design
2013-05-23 | E-GEOD-38179 | biostudies-arrayexpress