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Expression Profile of R. capsulatus under heat and cold stress

ABSTRACT: The effects of temperature stress on transcriptome of purple non sulfur bacterium R. capsulatus were investigated by comparing expression profiles under optimum hydrogen production condition (30°C), heat (42°C) and cold (4°C) stress conditions.

ORGANISM(S): Rhodobacter capsulatus

PROVIDER: GSE53477 | GEO | 2013/12/19

SECONDARY ACCESSION(S): PRJNA232083

REPOSITORIES: GEO

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Expression Profile of R. capsulatus under heat and cold stress

Project description:The effects of temperature stress on transcriptome of purple non sulfur bacterium R. capsulatus were investigated by comparing expression profiles under optimum hydrogen production condition (30M-BM-0C), heat (42M-BM-0C) and cold (4M-BM-0C) stress conditions. Bacteria were grown anaerobically under continuous illumination (200 W/m2) in 150 ml volume photobioreactors at 30M-BM-0C for 48 hours. Then cold stress (4M-BM-0C) and heat stress (42M-BM-0C) were applied in parallel. For microarray analysis, RNA samples from 1.5x109 cells were collected after 2 hours and 6 hours of stress applications. A microarray chip for Rhodobacter capsulatus was not commercially available. For that reason, a GeneChipM-BM-. array was custom designed and manufactured by Affymetrix, Santa Clara, California. The nucleotide sequence of the bacterium is available in GenBank with the accession numbers CP001312 for the chromosome and CP001313 for the plasmid pRCB133. The feature size of the antisense DNA array was 11 micron and the format was 100-3660. A total of 4,052 probe sets for open reading frames (ORFs) and 200 intergenic sequences with longer than 300bp were placed on the microarray. The cDNA synthesis, labeling, and hybridization protocols were performed according to the Affymetrix Expression Analysis Technical Manual given for prokaryotic samples

2013-12-19 | E-GEOD-53477 | biostudies-arrayexpress

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Project description:The influence of different nitrogen sources on transcriptome of Purple non sulfur bacterium R. Capsulatus was investigated by comparing expression profile on 5mM ammonium chloride and 2 mM glutamate. Carbon source was 40mM acetate on both conditions. To study the effect of different acetate concentrations, 40mM and 80mM acetate were used with 2 mM glutamate as nitrogen source. Bacteria were grown anaerobically under continuous illumination (200 W/m2) in 150 ml volume photobioreactors at 30M-BM-0C. For microarray analysis, RNA samples were collected after 16h of inoculation from 1.5x109 cells. A microarray chip for Rhodobacter capsulatus was not commercially available. For that reason, a GeneChipM-BM-. array was custom designed and manufactured by Affymetrix, Santa Clara, California. The nucleotide sequence of the bacterium is available in GenBank with the accession numbers CP001312 for the chromosome and CP001313 for the plasmid pRCB133. The feature size of the antisense DNA array was 11 micron and the format was 100-3660. A total of 4,052 probe sets for open reading frames (ORFs) and 200 intergenic sequences with longer than 300bp were placed on the microarray. The cDNA synthesis, labeling, and hybridization protocols were performed according to the Affymetrix Expression Analysis Technical Manual given for prokaryotic samples

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