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RNA expression for ethanologenic Escherichia coli strain LY180 in the absence and presence of 15 mM furfural for 15 min

ABSTRACT: The data explore the transcriptional response of strain LY180 to 15 mM furfural under anaerobic fermentation conditions. The expression differences of oxidoreductase in LY180 are described. Total RNA was prepared from cultures of LY180 immediately before and 15 min after addition of furfural to 15 mM. The NimbleGen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.

ORGANISM(S): Escherichia coli

SUBMITTER: Xuan Wang

PROVIDER: E-GEOD-34956 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA expression for ethanologenic E coli strains LY180, EMFR9 and EMFR35 in the absence and presence of 5mM and 15 mM furfural for 15 min

Project description:The data explore the transcriptional response of strains LY180 and EMFR9 to 5 mM furfural under anaerobic fermentation condition The data explore the transcriptional response of strains LY180 and EMFR35 to 15 mM furfural under anaerobic fermentation condition The expression differences of polyamine transporters in LY180 vs EMFR9 and EMFR35 are further described in RD Geddes,X Wang, LP Yomano, EN Miller, H Zheng, KT Shanmugam, and LO Ingram. 2013. Selected Polyamines and Polyamine Transporters Increase Furfural Tolerance (in preparation for submission to Appl Env Microbiol) Total RNA was prepared from cultures of LY180, EMFR9 and EMFR35 immediately before and 15 min after addition of furfural (5mM and 15 mM). The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene. The complete dataset comprising 8 samples is linked below as a supplementary file.

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Project description:The data explore the transcriptional response of strain LY180 and the furfural-resistant derivative EMFR9 to 0.5 g/L furfural LY180 and EMFR9 and differences in their expression profiles are described in Miller, E. N., L. R. Jarboe, L. P. Yomano, S. W. York, K. T. Shanmugam, and L. O. Ingram. 2009. Silencing of NADPH-dependent oxidoreductase genes (yqhD and dkgA) in furfural-resistant ethanologenic Escherichia coli. Appl Environ Microbiol 75:4315-23. The response of LY180 to furfural is described in Miller, E. N., L. R. Jarboe, P. C. Turner, P. Pharkya, L. P. Yomano, S. W. York, D. Nunn, K. T. Shanmugam, and L. O. Ingram. 2009. Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol., 2009. Total RNA was prepared from cultures of LY180 and EMFR9 immediately before and 15 min after addition of furfural to 0.5 g/L. The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene. Data from replicate 1 (OID 8641) and replicate 2 (OID 14117) was analyzed independently.

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