Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Adaptive laboratory evolution of a genome-reduced Escherichia coli

ABSTRACT: Adaptive laboratory evolution of a genome-reduced Escherichia coli

PROVIDER: PRJEB21199 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2001770.fastq.gz	Fastqsanger.gz
	ERR2002450.fastq.gz	Fastqsanger.gz
	ERR2001771.fastq.gz	Fastqsanger.gz
	ERR2001831.fastq.gz	Fastqsanger.gz
	ERR2002451.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 55

Similar Datasets

Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies

Project description:To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.

2017-06-21 | GSE89685 | GEO

Adaptive laboratory evolution of E. coli pdhR gene deletion strain

Project description:We have performed adaptive laboratory evolution of E. coli pdhR gene deletion strain to examine the adaptive strategies of E. coli.

2021-03-08 | GSE167389 | GEO

Adaptive laboratory evolution of E. coli ndh gene deletion strain

Project description:We have performed adaptive laboratory evolution of E. coli ndh gene deletion strain to examine the adaptive strategies of E. coli.

2023-09-12 | GSE242875 | GEO

Adaptive laboratory evolution with heterologous pgi

Project description:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after knockout of endogenous glucose-6-phosphate isomerase (pgi) and subsequent expression of heterologous version of the pgi gene from Pseudomonas aeruginosa and Bacillus megaterium.

2023-02-09 | GSE224989 | GEO

Adaptive laboratory evolution of chorismate synthase knockouts

Project description:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after chorismate synthase knockouts. Either isochorismate synthase (menF) or isochorismate synthase AND chorismate lyase (ubiC) was deleted from a strain of E. coli K-12 MG1655 that had already been previously adapted for growth on glucose minimal media. RNA-seq profiles of the original glucose-adapted strain, the 2 deletion strains, and 4 laboratory-evolved strains from each deletion are included in duplicate. ubiC catalyzes the first committed step of ubiquinone synthesis, an important molecule for the electron transport chain. Thus, these experiments allowed assessment of cellular adaptations to restore energy metabolism capability.

2023-02-08 | GSE224889 | GEO

Simultaneous in vivo enzyme and host engineering through laboratory evolution

Project description:Two genetic selection systems that couple metabolite hydroxylation or methylation of small molecules to growth of Escherichia coli are presented in this study. One system targets pterin-dependent hydroxylation (tBPt) while another focuses on S-adenosylmethionine-dependent methylation (SAM). Using adaptive laboratory evolution with growth selection, these two systems are demonstrated to not only achieve in vivo directed evolution of enzymes involved in human hormone biosynthesis but also reveal non-intuitive host factors that elude existing synthetic biology approaches. Raw sequencing data for the relevant strains generated in this study are presented here.

2019-01-30 | E-MTAB-6779 | biostudies-arrayexpress

Adaptive laboratory evolution with heterologous pgi

Project description:Adaptive laboratory evolution with heterologous pgi

| PRJNA933234 | ENA

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

Project description:We generated four strains of Escherichia coli K12 MG1655 with distinct proton motive force generation potential and performed the adaptive laboratory evolution of these strains to study how the system adapts to the loss of alternate electron transfer pathways of the Electron Transport System. RNA-Seq was performed to examine the underlying transcriptional rewiring.

2022-05-06 | GSE202144 | GEO

Adaptive Laboratory Evolution of E. coli towards usage of fluoroindole

Project description:Although fluorine is abundant in the earth’s crust, it is scarcely found in biomolecules. Adaptive laboratory evolution (ALE) experiments were conducted to introduce organofluorine into living microorganisms. By cultivating Escherichia coli with fluorinated indole analogs, microbial cells evolved that relinquished their dependence on indole and are instead capable of utilizing either 6-fluoroindole (6Fi) or 7-fluoroindole (7Fi) for growth (TrpS-catalyzed in-situ conversion of fluoroindole into fluorotryptophan (FTrp) and TrpRS-catalyzed incorporation of FTrp in context of protein biosynthesis). Consistent and complete adaptation of microbial populations was achieved and the quantitative proteome-wide replacement of Trp by either 6FTrp or 7FTrp was confirmed by nano-LC-MSMS. The dataset comprises the ancestral strain TUB00, two positive controls W-TUB165 and Ind-TUB165 (adapted to grow on tryptophan and indole), three 6Fi adapted lineages 6TUB128-OC, 6TUB165-MB4, 6TUB165-MB3 and two 7Fi adapted lineages 7TUB165-OC and 7TUB165-MB.

2024-01-08 | PXD048225 | Pride

Generation of Escherichia coli Enhanced Acetate Utilization through Compensatory ATP Consumption via Adaptive Laboratory Evolution

Project description:We carried out adaptive laboratory evolution of an E. coli strain lacking four genes (adhE, pta, ldhA, frdA) involved in acetyl-CoA consumption, allowing the efficient utilization of acetate as its sole carbon and energy source. The transcriptomes according to the medium status (M9 aceate, M9 glucose) of the evolved strain (SBA01) and its parent strain (DSM01) were compared using RNA-seq.

2020-09-15 | GSE157942 | 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