Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Response of Escherichia coli to acetate concentration during growth on glucose

ABSTRACT: E. coli MG1655 was grown on M9 minimal medium supplemented with 15mM glucose and either 0, 10, 50 or 100 mM acetate. Transcriptomic analysis from exponential growing cells was performed using Agilent microarray A-MEXP-2232. This work was done with the help of students during practicals. Consequently, it is of special interest since we have four biological replicates done over four years and two technical replicates per biological replicate (n=8 per condition). We therefore thank all the INSA-Toulouse students that participated in this project: Leidy Caraballo, Xavier Caron, Pauline Chanut, Sarah Guiziou, Ngoc Thu Hang Pham, Diane Barbay, Céline Ben Hassen, Thomas Cerutti, Cécile Roland, Sarah Srour, Audrey Baylet, Mathilde Beraud, Claudie Bosc, Lilas Courtot, Violaine Dolfo, Anna Kaci, Manon Chevallot-Beroux, Sarah Colom, Fanny Leclerc, Zihan Liao, Grégoire Quinet and Mélina Vaurs.

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

SUBMITTER: Brice Enjalbert

PROVIDER: E-MTAB-9086 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Response of Escherichia coli to acetate in presence of 100 mM methyl α-D-glucopyranoside

Project description:This experiment was performed to challenge E. coli response to acetate when its growth rate flux is reduced by 40% with 100 mM methyl α-D-glucopyranoside. Control without inhibition in the exact same conditions was already published on ArrayExpress database (accession number E-MTAB-9086) and could be used for comparison purpose. Here, E. coli BW25113 strain was grown in M9 medium complemented with 15 mM glucose, 100 mM αMG, and 0, 10, 50 or 100 mM sodium acetate. The cells were grown to mid-exponential phase in shake flasks at 37 °C and 200 rpm, in 50 mL of medium before proceeding to RNA extraction and subsequent microarray analysis. Three to four replicates (with two to three biological replicates) were analyzed for each condition. We thank all the INSA-Toulouse students that participated in this project: Lola Blayac, Romane Ducloux, Benjamin Jung, Oliver Larousse, Leyre Sarrias, Arno Bruel, Alexis Charbinat, Justine Dumas-Perdriau, Solène Frapard, Sophie Germain, Nicolas Papadopoulos, Marine Rodeghiero & Auriane Thomas.

2022-09-23 | E-MTAB-11717 | biostudies-arrayexpress

Methanol effect on an E. coli BW25113 strain expressing heterologous mdh and das enzymes during or after growth on xylose

Project description:In this project we used the strain E. coli BW25113 ΔfrmA::frt (Δ(araD-araB)567, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, hsdR514, ΔfrmA(::frt)) from the Keio collection (Baba et al. 2006). The plasmid {pSEVA424_mdh-das} (Low-copy-number, lacIq/Ptrc promoter, RK2 ori, SmR) from Silva-Rocha et al. 2013 was integrated in the strain to express mdh (Methanol dehydrogenase) and das (Dihydroxyacetone synthase) respectively from Acinetobacter gerneri and Pichia angusta. In this experiment, we inoculated 50 mL of M9 minimal medium with 15 mM xylose and with or without 0.15 M methanol, in baffled flasks at 30°C, 150 rpm. At D600=1 and D600=2, 12mL of each culture were centrifuged 1’30 at 14000 rpm before discarding the supernatant and freezing the pellets for 15 sec in liquid nitrogen. RNA extraction were carried out using a RNeasy Midi Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol and the transcriptomic experiments were run at the GeT-Biopuces Platform (Toulouse, France). Prior to the experiment, the quality of the RNA extracted was analyzed by Nanodrop and Cell Bio Analyser (Agilent Technologies, California, USA). The labelling with Cy3, hybridation on the Agilent chip and wash were carried out accordingly to the Agilent protocol and kits. We used the scanner NimbleGen MS 200 (Roche, Bâle, Suisse) with the following parameters: autogain, 5micros resolution, 532nm scan. The Agilent Feature Extraction software was used to extract the data.

2020-07-10 | E-MTAB-8909 | biostudies-arrayexpress

Transcriptional pattern of E. coli BW25113 and its ptsA, glpK and dhaKLM isogenic mutants growing on DHA (dihydroxyacetone).

Project description:Dihydroxyacetone (DHA) is an attractive molecule produced in a wide range of industries . DHA is found among all the kingdoms as an intermediate of various metabolic pathways and can be used as a carbon source by many organisms. The bacterium Escherichia coli is able to grow on DHA as the sole carbon source albeit at a low growth rate (0.1 h-1). If the topology of DHA metabolic network has been characterized, the function and regulation of the metabolic pathways involved in DHA metabolism remain unsolved. Here, we aimed to better understand DHA metabolism in E. coli BW25113 by exploring its transcriptional pattern on DHA versus glucose. We also studied the pattern of three DHA pathway mutants (dhaKLM, ptsA and glpK).

2019-06-03 | E-MTAB-7666 | biostudies-arrayexpress

Analysis of aortic gene expression in ovariectomized ApoE-deficient mice substituted with medroxyprogesterone acetate, norethisterone acetate or placebo

Project description:Agilent 4x44k Whole Mouse Genome v1 Microarrays were used to analyze aortic transcriptome of mice substituted with medroxyprogesterone acetate, norethisterone acetate or placebo after having been ovariectomized. The aim of this experiment was to detect genes regulated in the gestagen-treated groups as compared to placebo that might be involved in thrombotic events Aortic gene expression was analyzed in ApoE-deficient mice after ovariectomy and 90 days of hormone- or placebo-treatment (medroxyprogesterone acetate or norethisterone acetate) and feeding a high-fat Western-type diet.

2014-06-30 | E-GEOD-57972 | biostudies-arrayexpress

Candida albicans induces monocyte training via epigenetic programming through a dectin 1-dependent pathway

Project description:Non-specific protective effects against reinfection have been described following infection with Candida albicans. Here we show that mice defective in functional T and B lymphocytes were protected against reinfection with C. albicans in a monocyte-dependent manner. C. albicans and beta glucans induced functional programming of monocytes, leading to enhanced cytokine production in vivo and in vitro. The training required the beta glucan receptor dectin 1 and the non-canonical Raf 1 pathway. Monocyte training by beta-glucans was mediated by epigenetic mechanisms through genome-wide changes in histone trimethylation at H3K4. Pathway analysis showed specific induction of epigenetic changes in genes of innate immunity. The functional programming of monocytes, reminiscent of similar properties of NK cells, has been termed M-bM-^@M-^\trained immunityM-bM-^@M-^] and may be employed for the design of improved vaccination strategies. Chromatin-IP at day7 followed by highthroughput sequencing to look at the differences in H3K4me3 and H3K27me3 binding in Monocytes either cultured in RPMI only versus those trained for 24hrs with beta glucan. Additionally expression analysis was performed by doing strandspecific RNAseq also for both unstimulated and beta glucan trained monocytes for correlating the histone modification changes with the expression changes. Biological replicates were generated from independent samples for H3K4me3 and RNAseq. Additional H3K4me3 ChIP-seq assays were performed for day0 untreated, 24hrs control and beta glucan trained monocytes. H3K4me3 ChIP-seq was also performed for Mouse macrophages both saline(control) and low dose Candida treated.

2012-12-21 | E-GEOD-34260 | biostudies-arrayexpress

Effect of FadR overexpression in an engineered fatty acid overproducer

Project description:Transcriptome analysis of strains LT-ΔfadE (control) and FRT-ΔfadE (FadR overexpressor) after 12h of fatty acid production. The strains used are described in detail in Zhang F, M Ouellet, TS Batth, CJ Petzold, A Mukhopadhyay and JD Keasling. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. (In preparation) Three independent cultures of control strain LT-ΔfadE and four independent cultures of FadR overexpressor strain FRT-ΔfadE were induced. One sample derived from each culture was hybridized.

2012-01-28 | E-GEOD-35392 | biostudies-arrayexpress

Osteoblast primary cell lines (OBS) from Shwachman-Diamond Syndrome (SDS) patients compared to healthy donors by one color transciptome array

Project description:The idea was to evaluate the transcriptome differences between osteoblasts derived from SDS patients compared to healthy donors and especially to enlighten the bone-related genes deregulation. The aim was to identify genes involved in SDS-related bone defects.

2020-08-15 | E-MTAB-9397 | biostudies-arrayexpress

Relating differences in the colonisation potential of verotoxigenic Escherichia coli (VTEC) for plant hosts to wholescale genes in gene expression

Project description:Verotoxigenic Escherichia coli (VTEC) are a leading cause of food-borne illness. Fruit and vegetables are recognised as an important source of the pathogen and can account for ~ 25 % of food-borne VTEC outbreaks, globally. The ability of VTEC to colonise leaves and roots of leafy vegetables, spinach (Spinacia oleracea) and lettuce (Lactuca sativa), was compared. The highest levels of colonisation occurred in the roots and rhizosphere, whereas colonisation of the leaves was lower and significantly different between the species. Colonisation of the leaves of prickly lettuce (L. serriola), a wild relative of domesticated lettuce, was especially poor. Differential VTEC gene expression in spinach extracts was markedly different for three tissue types, with little overlap. Comparison of expression in the same tissue type, cell wall polysaccharides, for lettuce and spinach also showed substantial differences, again with virtually no overlap. The transcriptional response was largely dependent on temperatures that are relevant to plant growth, not warm-blooded animals. The data show that VTEC adaptation to plant hosts and subsequent colonisation potential is underpinned by wholescale changes in gene expression that are specific to both plant tissue type and to the species.

2016-08-01 | E-MTAB-3249 | biostudies-arrayexpress

Microarray of porcine samples after repairing using tissue engineering graft

Project description:After implantion into porcine condyles at knee, the samples were harvested and the RNA was attracted, the RNA harvested was compared to all native surrounding tissues to study the phenotype of the regenerated cartilaginous tissue.

2020-05-17 | E-MTAB-7986 | biostudies-arrayexpress

Design of a gene signature to assess the proinflammatory and the profibrotic polarization of murine fibroblasts

Project description:We provide an original multi-stage approach identifying a gene signature to assess the fibroblast polarization. Prototypic polarizations (inflammatory/fibrotic) were induced by seeded mouse embryonic fibroblasts (MEFs) with TNFα or TGFß1, respectively. The transcriptomic and proteomic profiles were obtained by RNA microarray and LC/MS-MS. Gene Ontology and pathways analysis were performed among the differentially expressed genes (DEGs) and proteins (DEPs). Balb/c mice underwent daily intradermal injections of HOCl (or PBS) as an experimental murine model of inflammation-mediated fibrosis in a time-dependent manner. As results, 1,456 and 2,215 DEGs, and 289 and 233 DEPs were respectively found in MEFs in response to TNFα or TGFß1, respectively. Among the most significant pathways, we combined 26 representative genes to encompass the proinflammatory and profibrotic polarizations of fibroblasts. Based on principal component analysis, this signature deciphered baseline state, proinflammatory polarization, and profibrotic polarization as accurately as did RNA microarray and LC/MS-MS. Then, we assessed the gene signature on dermal fibroblasts isolated from the experimental murine model. We observed a proinflammatory polarization at day 7, and a mixture of a proinflammatory and profibrotic polarizations at day 42 in line with histological findings. Our approach provides a small-size and convenient gene signature to assess murine fibroblast polarization.

2022-07-12 | PXD034078 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data