Geobacter metallireducens GS-15 chemostat cultures were grown at 30°C with a dilution rate of 0.05 h-1 and with 55 mM ferric citrate as the electron acceptor. The electron donor was limiting, and was 1.25 mM benzoate.
Biomaterial provider
Derek Lovley Lab at the Department of Microbiology at the University of Massachusetts Amherst
Treatment protocol
Benzoate as the electron donor
Growth protocol
Esteve-Nunez, A., Rothermich, M. M., Sharma, M., Lovley, D. R. 2005. Growth of Geobacter sufurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7(5):641-648.
Extracted molecule
total RNA
Extraction protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.
Label
Cy5
Label protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.
Channel 2
Source name
Geobacter metallireducens with acetate as electron donor
Geobacter metallireducens GS-15 chemostat cultures were grown at 30°C with a dilution rate of 0.05 h-1 and with 55 mM ferric citrate as the electron acceptor. The electron donor was limiting, and was 5 mM acetate.
Biomaterial provider
Derek Lovley Lab at the Department of Microbiology at the University of Massachusetts Amherst
Treatment protocol
Acetate as the electron donor
Growth protocol
Esteve-Nunez, A., Rothermich, M. M., Sharma, M., Lovley, D. R. 2005. Growth of Geobacter sufurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7(5):641-648.
Extracted molecule
total RNA
Extraction protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.
Label
Cy3
Label protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.
Hybridization protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.
Scan protocol
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.
Description
The objective of the experiment is to compare the gene expression profiles of Geobacter metallireducens given different electron donors, i.e. benzoate and acetate, under iron-reducing growth conditions.
Data processing
He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.
