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Vibrio cholerae Freezing Study

ABSTRACT: 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.

ORGANISM(S): Vibrio cholerae

PROVIDER: GSE38179 | GEO | 2013/05/23

SECONDARY ACCESSION(S): PRJNA167440

REPOSITORIES: GEO

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Vibrio cholerae Freezing Study

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

Transcription profiling of human oral lesions treated with bioadhesive black rasberry gel to determine the effect on gene expression and proinflammatory proteins

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Project description:These experiments were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VC73-orf6/7-Kan-A was added after 24h and the cells grown further for 24h. The VC73-orf6/7-Kan-A strain is a ATCC25873 derivative (both O37 serogroup) which harbors a Kanamycin cassette in the O37 region (as part of the operon between orf6 and orf7 w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Three clones were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. Comparison of A1552 versus VC73-orf6/7-Kan-A is shown as control. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design

2007-04-26 | GSE5935 | GEO

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