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Hi-C study of the E. coli MG1655 chromosome

ABSTRACT: 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.

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

PROVIDER: GSE61658 | GEO | 2015/09/01

SECONDARY ACCESSION(S): PRJNA261786

REPOSITORIES: GEO

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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

Gene expression of E. coli MG1655 wild type and rpoS knock-out strains

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Time-course gene expression profiles to understand compositional changes of the E. coli K-12 MG1655 transcriptiome during the transition from the exponential growth to the stationary phase

Project description:Time-course gene expression profiles to understand compositional changes of the E. coli K-12 MG1655 transcriptiome during the transition from the exponential growth to the stationary phase

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Transcription profiling of E. coli MG1655 wild type and rpoS knock-out strains

Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Experiment Overall Design: Affymetrix E. coli antisense genome array was used to compare the gene expression among E. coli wild type and rpoS konck-out strains in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. All samples were grown in MOPS minimal media with 0.2% glucose. Biofilms were grown for 72 hours on glass surface in flow cells (1x4x40 mm), and planktonic cells were grown for 8 hours (exponential phase) and 12 hours (stationary phase). Experiments were repeated 3 times, which resulted in 3 replicates of 6 different samples.

2008-06-18 | E-GEOD-7885 | biostudies-arrayexpress

Transcription profiling by array of E. coli MG1655 strains with deletions of fis and hns in early-exponential, mid-exponential, transition-to-stationary and stationary phases

Project description:Differential expression of genes in E. coli MG1655 strains with deletions of fis and hns was assessed under early-exponential, mid-exponential, transition-to-stationary and stationary phases of growth in LB medium.

2010-09-01 | E-MEXP-2838 | biostudies-arrayexpress

Transcriptomic differences between E. coli B REL606 and K-12 MG1655

Project description:Transcriptome profiles were analyzed using the samples taken at the exponential and stationary phases during the cultivation of REL606 and MG1655 in LB medium. At the exponential growth phase, most highly expressed genes of B were those for replication, translation, or nucleotide transport and metabolism, while many of the K-12 genes were involved in cell motility, transcription, carbohydrate transport, or energy production. At the stationary phase, many of the genes highly expressed in B were for transport and metabolism of various amino acids and carbohydrates, whereas those in K-12 had functions related to cell motility, ribosomal subunit protein production, or energy generation. Many genes in REL606 and MG1655 showed highly distinct expression levels irrespective of growth conditions. Highly expressed genes in REL606 included those encoding enzymes for biosynthesis of L-arginine (argAGDECBHI) and branched-chain amino acid (ilvGMEDA), and those encoding a subunit of the L-arginine transporter (artJ), cytochrome b562 (cybC), subunits of the histidine ABC transporter (hisPJ), cytotoxins (hokED), outer membrane porin (ompF), L-arginine decarboxylase (speA), and cell division inhibitor (sulA). Highly expressed genes in MG1655 included those for chemotaxis (cheZYRWA, tap, trg, tsr), Lon protease (lon), C4-dicarboxylate-sensing histidine kinase (dcuS), chaperones (clpB, dnaK, groES, htpG, ibpA), the major subunit of type 1 fimbriae (fimA), a regulator of flagellar biosynthesis (flhC), glycerol-3-phosphate-dehydrogenase (glpABCD), glycerophosphoryl diester phosphodiesterase (glpQ), glycerol-3-phosphate transporter (glpT), hydrogenase 2 (hybCBO), outer membrane porins (nmpC, ompA, ompC), and galactitol transport and metabolism (gatYZC).

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Stationary phase in LB, genomic DNA reference

Project description:Responses of Escherichia coli MG1655 in stationary phase in LB Keywords: time course

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Transcriptome analysis of E.coli MG1655 under multiple growth conditions

Project description:Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and nitrogen-limiting condition. A fourteen chip study using total RNA recovered from four separate culture conditions of E.coli K12 MG1655. E.coli strains were harvested at mid-exponential phase with exception of stationary phase experiments. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome (NimbleGen). Experiments were conducted as three or more biological replicates (different cultures)

2009-11-03 | E-GEOD-15534 | biostudies-arrayexpress

Genome-wide RNA-sequencing of E. coli strain 55989 from in vitro and in vivo samples

Project description:RNA-seq comparative analysis of an enteroaggregative Escherichia coli human isolate grown in vitro and in vivo (colon samples from monocolonized mice) revealed candidates genes that are either overexpressed or underexpressed. Comparisons included exponential growth vs stationary growth; exponential vs colon and stationary vs colon.

2021-01-28 | GSE165634 | GEO

MG1655 araC arabinose transcription profiling

Project description:AraC is an Escherichia coli transcription factor that regulates genes in response to the presence/absence of arabinose. We used transcription profiling to determine RNA levels in Escherichia coli K-12 strain MG1655 and MG1655 delta araC grown either in the absence or the presence of arabinose. Thus, we identified known and novel AraC-regulated genes. Data presented here are raw .CEL files as well as fully analysed data using GeneSpring

2013-10-19 | E-MTAB-1916 | biostudies-arrayexpress

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