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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Escherichia coli planktonic cultures: mono-species culture vs. mixed-species culture

ABSTRACT: Transcription profile of Escherichia coli cells in mono-species pure planktonic cultures was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species planktonic cultures E. coli cells were separated from dual-species planktonic cultures before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli planktonic cultures were processed with the same separation protocol before RNA extraction. Two condition experiments: E. coli mono-species pure planktonic culture vs E. coli in mixed-species planktonic cultures. Two biological replicates with independently grown and harvested planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.

ORGANISM(S): Escherichia coli K-12

SUBMITTER: Dongjuan Dai

PROVIDER: E-GEOD-24913 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Escherichia coli planktonic cultures: mono-species culture vs. mixed-species culture

Project description:Transcription profile of Escherichia coli cells in mono-species pure planktonic cultures was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species planktonic cultures E. coli cells were separated from dual-species planktonic cultures before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli planktonic cultures were processed with the same separation protocol before RNA extraction.

2013-12-30 | GSE24913 | GEO

Identifying genes of Escherichia coli involved in interactions with Stenotrophomonas maltophilia in planktonic cultures and biofilms using transcriptomic analysis

Project description:Biofilm formation by Escherichia coli was significantly inhibited when co-cultured with Stenotrophomonas maltophilia in static systems. Genes of E. coli involved in species interactions with S. maltophilia were identified in order to allow the study of the mechanisms of inhibited E. coli biofilm formation in co-culture. A total of 89 and 108 genes were identified as differentially expressed in mixed species cultures when growing as biofilm and as planktonic cultures, respectively, compared to the counterpart of pure cultured E. coli. Differential expression of certain identified genes was confirmed using E. coli reporter strains combined with single-cell based flow cytometry analysis. Co-culture with S. maltophilia affected genes involved in metabolism, signal transduction, cell wall composition, and biofilm formation of E. coli. Several selected genes were further confirmed as affecting E. coli biofilm formation in mixed species cultures with S. maltophilia. The data suggest that these genes were involved in species interactions between E. coli and S. maltophilia. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.

2013-12-30 | E-GEOD-24915 | biostudies-arrayexpress

Escherichia coli biofilm: mono-species culture vs. mixed-species culture

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2013-12-30 | E-GEOD-24912 | biostudies-arrayexpress

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Escherichia coli cells: sorted vs. non-sorted

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Escherichia coli biofilms vs planktonic culture

2013-12-30 | GSE24914 | GEO

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