Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Toward industrial C8 production: Oxygen intrusion drives renewable n-caprylate production from ethanol and acetate via intermediate metabolite production

PROVIDER: PRJNA1137092 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29876923_1.fastq.gz	Fastqsanger.gz
	SRR29876924_1.fastq.gz	Fastqsanger.gz
	SRR29876925_1.fastq.gz	Fastqsanger.gz
	SRR29876926_1.fastq.gz	Fastqsanger.gz
	SRR29876927_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Tolerance mechanisms towards high-temperature and -acid stress conditions during itaconic acid biosynthesis in Aspergillus terreus

2015-09-16 | GSE73033 | GEO

Stabilized biological production by product addiction

Project description:Populations of engineered metabolite-producing microorganisms are prone to evolutionary production declines during industrial-scale cultivations. In this study, we develop a synthetic product addiction system in E coli that addicts mevalonic acid production cells to mevalonic acid. Through experimentally simuluated long-term fermentation, we investigate how product-addicted organisms remain stable and avoid formation of genetic subpopulations of fit, non-producing cells.

2018-02-09 | E-MTAB-6182 | biostudies-arrayexpress

Tolerance mechanisms towards high-temperature and -acid stress conditions during itaconic acid biosynthesis in Aspergillus terreus

Project description:A. terreus LYT10 is an industrial strain for itaconic acid production, in which the biosynthesis of itaconic acid and glucose conversion rate were affected by temperature and initial concentration of itaconic acid in industrial production. RNA-seq was used to identify the key regulators related to tolerance mechanism toward various stress conditions. A total of 4 samples were analzyed. The mycelia cultivated in itaconic acid production medium (IPM) on a rotary shaker at 220 rpm and 37°C for 36 h was considered as a reference. IPMs with 5 g/L and 40 g/L itaconic acid (pH 3.25) were used for high-acid culture respectively. High-temperature condition was possesed at 42°C for 36 h in IPM.

2015-09-16 | E-GEOD-73033 | biostudies-arrayexpress

Angenent Lab Substrate Ratio Carboxylate Platform

Project description:Higher substrate ratios of ethanol to acetate steered chain elongation toward n-caprylate in a bioreactor with product extraction

| PRJEB21834 | ENA

Aerobic Adaptation and Metabolic Dynamics of Propionibacterium freudenreichii DSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis

Project description:Propionibacterium freudenreichii (PFR) DSM 20271 is a bacterium known for its ability to thrive in diverse environments and produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271 to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably B12 vitamin, pseudovitamin-B12, propionate and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, TCA cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for sensing and adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and α-ketoglutarate availability. Furthermore, in liquid culture, FeSO4 supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding of PFR's physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications.

2024-09-09 | PXD051703 | Pride

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.

2013-12-10 | GSE53140 | 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

Standardized generation of human iPSC-derived hematopoietic organoids and macrophages utilizing a benchtop bioreactor platform under fully defined conditions

Project description:There is a significant demand for intermediate-scale bioreactors in academic and industrial institutions to produce cells for various applications in drug screening and/or cell therapy. However, the application of these bioreactors in cultivating hiPSC-derived immune cells and other blood cells is noticeably lacking. To address this gap, we have developed a xeno-free and chemically defined intermediate-scale bioreactor platform, which allows for the generation of standardized human iPSC-derived hematopoietic organoids and subsequent continuous production of macrophages (iPSC-Mac).

2024-05-29 | GSE268458 | GEO

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

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

Genome resequencing data of adaptive laboratory evolved E. coli W

Project description:Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we found spontaneous mutations in the conserved regions of AC and CRP.

2021-08-23 | GSE162596 | 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