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Dynamic transcriptome structure of E. coli K-12 MG1655 across growth

ABSTRACT: High-resolution transcriptional profiling of E. coli across nine timepoints of growth in rich media (LB). Samples collected from lag phase to stationary phase of growth. High-resolution tiling array to detect conditional operon isoforms. Custom Agilent array designed to detect condition-specific transcriptional isoforms. Array designed for E coli K12 MG1655 genome. Tiled using 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites at 6 bp resolution. Nine growth time points in the experiment. Two-color arrays. Each time point compared to mid-exponential phase of growth.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Aaron Brooks

PROVIDER: E-GEOD-55879 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A system-level model for the microbial regulatory genome.

Brooks Aaron N AN Reiss David J DJ Allard Antoine A Wu Wei-Ju WJ Salvanha Diego M DM Plaisier Christopher L CL Chandrasekaran Sriram S Pan Min M Kaur Amardeep A Baliga Nitin S NS

Molecular systems biology 20140715

Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional infl ...[more]

PMID: 25028489

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Dynamic transcriptome structure of E. coli K-12 MG1655 across growth

Project description:High-resolution transcriptional profiling of E. coli across nine timepoints of growth in rich media (LB). Samples collected from lag phase to stationary phase of growth. High-resolution tiling array to detect conditional operon isoforms. Custom Agilent array designed to detect condition-specific transcriptional isoforms. Array designed for E coli K12 MG1655 genome. Tiled using 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites at 6 bp resolution.

2014-07-22 | GSE55879 | GEO

RNA sequencing based analysis of the bacterial transcriptome

Project description:To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media (carbon, nitrogen, or phosphate limited) and the total transcriptome of log and stationary phase samples was sequenced.

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Hi-C study of the E. coli MG1655 chromosome

Project description:We performed Hi-C analysis of Escherichia coli MG1655 cells in exponential and stationary growth phase. We could detect long-range interactions predominantly in the Ori domain of the chromosome. Interestingly, the use of a new type of control revealed that these interactions are mostly crosslinking independent. 6 samples from exponential phase growth in M9 medium; 6 samples from stationary phase growth in M9 medium; for each growth condition, 3 samples were with crosslinking and 3 samples were without.

2015-09-01 | E-GEOD-61658 | biostudies-arrayexpress

Unexpected complexity of the Escherichia coli K-12 transcriptome architecture revealed by single nucleotide resolution RNA sequencing

Project description:To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media and the total transcriptome of log and stationary phase samples was sequenced.

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Project description:Total RNA was extracted and sequenced from Escherichia coli cultured to log phase and stable phase at 37 ° C and 45 ° C, respectively. The transcriptome data of Escherichia coli under four different growth conditions were obtained.

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Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)

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