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ABSTRACT:
PROVIDER: PRJNA741373 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptional profiling comparing Escherichia coli simultaneously exposed to tellurite and CTX with untreated control cells; Tellurite with control; CTX with control Three-condition experiment, antibacterial (tellurite; CTX or tellurite/CTX) vs. Untreated control cells. Biological replicates: 3 control, 3 toxicants exposed cells, independently grown and harvested. One replicate per array.
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Project description:Reed2003 - Genome-scale metabolic network of
Escherichia coli (iJR904)
This model is described in the article:
An expanded genome-scale
model of Escherichia coli K-12 (iJR904 GSM/GPR).
Reed JL, Vo TD, Schilling CH,
Palsson BO.
Genome Biol. 2003; 4(9): R54
Abstract:
BACKGROUND: Diverse datasets, including genomic,
transcriptomic, proteomic and metabolomic data, are becoming
readily available for specific organisms. There is currently a
need to integrate these datasets within an in silico modeling
framework. Constraint-based models of Escherichia coli K-12
MG1655 have been developed and used to study the bacterium's
metabolism and phenotypic behavior. The most comprehensive E.
coli model to date (E. coli iJE660a GSM) accounts for 660 genes
and includes 627 unique biochemical reactions. RESULTS: An
expanded genome-scale metabolic model of E. coli (iJR904
GSM/GPR) has been reconstructed which includes 904 genes and
931 unique biochemical reactions. The reactions in the expanded
model are both elementally and charge balanced. Network gap
analysis led to putative assignments for 55 open reading frames
(ORFs). Gene to protein to reaction associations (GPR) are now
directly included in the model. Comparisons between predictions
made by iJR904 and iJE660a models show that they are generally
similar but differ under certain circumstances. Analysis of
genome-scale proton balancing shows how the flux of protons
into and out of the medium is important for maximizing cellular
growth. CONCLUSIONS: E. coli iJR904 has improved capabilities
over iJE660a. iJR904 is a more complete and chemically accurate
description of E. coli metabolism than iJE660a. Perhaps most
importantly, iJR904 can be used for analyzing and integrating
the diverse datasets. iJR904 will help to outline the
genotype-phenotype relationship for E. coli K-12, as it can
account for genomic, transcriptomic, proteomic and fluxomic
data simultaneously.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180060.
To cite BioModels Database, please use:
BioModels Database:
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2015-07-30 | MODEL1507180060 | BioModels
Project description:Distribution of RNAP beta' subunit (RpoC) on genomic sites was studied for exponentially growing Escherichia coli using ChIP-Seq.
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Project description:Distribution of topoisomerase I (EcTopoI) on genomic sites was studied for exponentially growing Escherichia coli in different conditions using ChIP-Seq.
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Project description:This study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) organization of the bacterial genome. We used recently published Escherichia coli GapR ChIP-seq and TopoI ChIP-seq (also called EcTopoI-seq) data, which marks positive and negative supercoiling sites, respectively, to study how supercoiling correlates with the spatial contact maps obtained from chromosome conformation capture sequencing (Hi-C and 5C). We find that supercoiled chromosomal loci have overall higher Hi-C contact frequencies than sites that are not supercoiled. Surprisingly, positive supercoiling corresponds to higher spatial contact than negative supercoiling. Additionally, positive, but not negative, supercoiling could be identified from Hi-C data with high accuracy. We further find that the majority of positive and negative supercoils coincide with highly active transcription units, with a minor group associated with replication and other genomic processes. Our results show that both positive and negative supercoiling enhance spatial contact, with positive supercoiling playing a larger role in bringing genomic loci closer in space. Based on our results, we propose new physical models of how the E. coli chromosome is organized by positive and negative supercoils.
2023-11-03 | GSE214856 | GEO
Project description:Primary objectives: The study investigates whether a Escherichia coli Nissle-suspenison has a (preventive) antidiarrheal effect in patients with tumors who are treated with chemotherapeutic schemes which are associated with increased occurances of diarrhea. Diarrhea caused by treatment are thought to be reduced in intensity and/or frequency by the treatment with Escherichia coli Nissle-Suspension.
Primary endpoints: Common toxicity criteria (CTC) for diarrhea
| 2534265 | ecrin-mdr-crc