Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Evolutionary Engineering of E. coli MG1655 for Tolerance Against Isoprenol

PROVIDER: PRJNA665813 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12717900_1.fastq.gz	Fastqsanger.gz
	SRR12717900_2.fastq.gz	Fastqsanger.gz
	SRR12717901_1.fastq.gz	Fastqsanger.gz
	SRR12717901_2.fastq.gz	Fastqsanger.gz
	SRR12717902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 44

Similar Datasets

Evolutionary Engineering of E. coli MG1655 for Tolerance Against Isoprenol

Project description:Evolutionary Engineering of E. coli MG1655 for Tolerance Against Isoprenol

| PRJNA667093 | ENA

DNA Microarray of Global Transcription Factor Mutant Reveals Membrane-Related Proteins Involved in n-Butanol Tolerance in Escherichia coli

Project description:We successfully isolated an E. coli strain harboring rpoD mutant B8 with 2% (v/v) butanol tolerance using global transcriptional machinery engineering approach. DNA microarrays were employed to assess the transcriptome profile of n-butanol tolerance strain B8 and control strain E. coli JM109. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.

2016-05-10 | GSE79305 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CRP-E182D Transcriptomes

Project description:Strain engineering for industrial production requires the improvement of tolerance to multiple unfavorable conditions. Here, we report using global regulator libraries based on the CRISPR-enabled trackable genome engineering (CREATE) method to engineer tolerance against multiple inhibitors in Escherichia coli. Deep mutagenesis libraries were rationally designed, constructed, and screened to target 34,340 mutations across 23 global regulators. A total of 69 specific mutations that respectively conferred tolerance to acetate, NaCl, furfural, and high temperature were isolated, confirmed, and evaluated. Among them, 32 novel reconstructed mutations exhibited better tolerance to the corresponding inhibitors, and the most dramatic mutation CRP-E182D conferred high cross-tolerance to acetate, NaCl and isobutanol. To further investigate the effects of this mutation in the CRP on acetate tolerance, whole-transcriptome sequencing (RNA-Seq) analysis was performed.

2024-03-01 | GSE199389 | GEO

ChIP-chip of MG1655 with antibody against E. coli RNAP beta subunit under various conditions

Project description:We integrated RNAP binding regions (RBRs) and mRNA transcript abundance to determine segments of contiguous transcription originating from promoter regions. To measure RBRs at a genome scale, we employed a ChIP-chip method to E. coli K-12 MG1655 grown in the presence or absence of rifampicin under multiple growth conditions using antibody against E. coli RNAP beta subunit.

2009-11-04 | GSE15588 | GEO

VirF gene from Shigella spp is able to induce chromosomal genes in E. coli

Project description:In order to understand whether the evolutionary acquisition of virF gene may have altered the transcriptional program in Shigella's harmless ancestor (E. coli) promoting the inactivation of genes potetially detrimental to the full expression of the invasivity phenotype, we performed a global transcriptional analysis of E. coli cells expressing or lacking the virF gene. To this end we used the E. coli K12 MG1655 strain, carrying the virF-encoding plasmid pMYSH6504, or its virF depleted derivative pMY6504R. Two condition experiment: the E. coli K12 MG1655 strain, carrying the virF-encoding plasmid pMYSH6504, and its virF depleted derivative pMY6504R. Two replicate for each condition

2011-06-25 | E-GEOD-30207 | biostudies-arrayexpress

Genome-scale reconstruction of the PurR regulon reveals its role in the adenine stimulon of Escherichia coli K-12 MG1655

Project description:This SuperSeries is composed of the following subset Series: GSE26588: Transcriptome analysis of E. coli MG1655 GSE26589: ChIP-chip of E. coli K-12 MG1655 with antibody against PurR-8myc under various conditions. Refer to individual Series

2012-01-12 | E-GEOD-26591 | biostudies-arrayexpress

VirF gene from Shigella spp is able to induce chromosomal genes in E. coli

2011-06-25 | GSE30207 | GEO

ArcA Chip-chip from Escherichia coli MG1655 K-12, WT and ∆arcA strains

Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli

2013-10-17 | GSE46413 | GEO

Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage

Project description:Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0. This analysis suggests that C8 challenge causes intracellular acidification and membrane damage. Escherichia coli MG1655 was grown to midlog (OD550 ~0.8) with or without 10 mM octanoic acid (pH=7.0) and the RNA was harvested and prepared for Affymetrix Microarray analysis.

2013-12-10 | E-GEOD-53140 | biostudies-arrayexpress

Expression profile of E. coli in response to exogenous addition of isopentenol

Project description:Exogenous isopentenol was added to a culture of E. coli and the RNA expression response was measured using Nimblegen arrays. Genes highly upregulated were then subsequently overexpressed to improve the tolerance to isopentenol toxicity. In addition a subset of genes that improved the tolerance were also overexpressed in a producing strain, leading to improved production over the empty vector control. This work is described in Foo et al, Improving microbial bio-gasoline production in E. coli using tolerance engineering (in preparation)

2013-12-10 | GSE53138 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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