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DNA microarray analysis of genes positively regulated by HapR

ABSTRACT: Vibrio cholerae strains A1552 and ATN140 (A1552-delta-hapR) were diluted 1:100 from over night cultures and grown aerobically (at 250 rpm) in M9 minimal medium supplemented with vitamins (MEM vitamin solution, BRL) and 0.5% lactate. At OD600 ~ 0.3 2 mM (GlcNAc)6 (Seikagaku America, East Falmouth, MA) was added and the cultures were further shaken for 2 hours. After harvesting the bacteria by centrifugation, the cell pellet was resuspended in Trizol reagent (GIBCO/BRL) and stored at -80 degrees C until further use. The procedure of RNA isolation and the corresponding amplicon microarray experiments was described by K. L. Meibom et al., Proc. Natl. Acad. Sci. U.S.A 101, 2524-9 (2004). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

ORGANISM(S): Vibrio cholerae

PROVIDER: GSE3576 | GEO | 2005/12/15

SECONDARY ACCESSION(S): PRJNA93657

REPOSITORIES: GEO

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DNA microarray analysis of genes positively regulated by HapR

Project description:Vibrio cholerae strains A1552 and ATN140 (A1552-delta-hapR) were diluted 1:100 from over night cultures and grown aerobically (at 250 rpm) in M9 minimal medium supplemented with vitamins (MEM vitamin solution, BRL) and 0.5% lactate. At OD600 ~ 0.3 2 mM (GlcNAc)6 (Seikagaku America, East Falmouth, MA) was added and the cultures were further shaken for 2 hours. After harvesting the bacteria by centrifugation, the cell pellet was resuspended in Trizol reagent (GIBCO/BRL) and stored at -80 degrees C until further use. The procedure of RNA isolation and the corresponding amplicon microarray experiments was described by K. L. Meibom et al., Proc. Natl. Acad. Sci. U.S.A 101, 2524-9 (2004). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed

2010-06-30 | E-GEOD-3576 | biostudies-arrayexpress

Transcription profiling of Vibrio cholerae wild type, hapR and rpoS deletions in mid-exponential or stationary phase concluding that rpoS controls the Vibrio cholerae mucosal escape response

Project description:For expression analysis of wild-type V. cholerae, hapR, and rpoS deletion mutants in mid-exponential or stationary phase, the strains were grown to either OD600 of 0.3 or for 11 h in LB media at 37 0C, and bacteria from 2-ml culture were quickly pelleted, resuspended in Trizol reagent (GIBCO/BRL, San Diego, California, United States), and frozen on dry ice. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. At least four microarray experiments were performed for each of two biological replicates for the tested strains. Gene expression of V. cholerae, rpoS, and hapR deletion mutants in stationary phase LB cultures was analyzed and compared to the wild-type parent under identical conditions. Gene expression of the wild-type parent during stationary phase after 11 h growth in LB was analyzed using RNA from an exponentially growing culture as a reference.

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Microarray analysis of gene expression in wt, rpoS and hapR mutants in stationary phase

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DNA microarray analysis of genes positively regulated by TfoX

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

DNA microarray analysis of genes positively regulated by TfoX

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 Î¼g/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. Computed

2010-06-30 | E-GEOD-3577 | biostudies-arrayexpress

Vibrio natriegens genome-scale metabolic modelling (GSMM) reveals insights into halophilic adaptations and resource allocation

Project description:Proteome profiles of Vibrio natriegens used for genome-scale metabolic modeling (GSMM). Profiling was performed across cell cultures grown aerobically on minimal medium. Cultures profiles were acquired across a range of salinities.

2023-02-07 | MSV000091219 | MassIVE

Vibrio natriegens genome-scale modelling reveals insights into halophilic adaptations and resource allocation

Project description:Proteome profiles of Vibrio natriegens used for genome-scale metabolic modeling (GSSM). Profiling was performed across cell cultures grown aerobically on minimal medium. Cultures profiles were acquired across a range of salinities.

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Ribosome profiling of E. coli K-12 MG1655 MOPS rich media with 0.2% glucose

Project description:Ribosome profiling was performed on E. coli wild type cells. All replicates were grown to an OD of ~0.4 in MOPS rich Media with 0.2% glucose supplemented, aerobically in shake flasks. Cultures were treated with chloramphenicol 2 min prior to harvest.

2015-06-09 | GSE63858 | GEO

Project description:MEM+TET

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BW25113 ymgB and W/T in LBglu 24h biofilm cells

Project description:For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms (30) in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures diluted that were 1:167. The cells were shaken at 250 rpm and 37°C for 24 hours to form biofilms on the glass wool, and RNA was isolated from the suspension cells and the biofilm. Keywords: E. coli biofilm

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