Ontology highlight
ABSTRACT:
PROVIDER: PRJNA750500 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We developed a mini-chemostat system with 16 reactors, each at a working volume of 40 ml. Sensors measure dissolved oxygen in the reactor, while OD600 is measured in the outflow. We further developed a CO2 and pH sensor array that can be plugged in to the outflow of the reactors. The system was used to characterize yeast physiology at four metabolically different conditions: limitations of glucose, both aerobic and anaerobic, nitrogen, and ethanol. The physiology of yeast cells grown at the four different conditions in the mini-chemostat (MC) system was compared with yeast cells grown in a DASGIP 1L system using RNAseq analysis
2019-02-01 | GSE120188 | GEO
Project description:Responses of Escherichia coli MG1655/pTrc99a(NOX-) grown at different growth rates in chemostat in M9 + salts Keywords: different growth rates in parallel
2006-03-08 | GSE4366 | GEO
Project description:RNA sequencing was performed on multiple E. coli strains grown on glucose minimal media
2019-12-17 | GSE122296 | GEO
Project description:Transcription profiles in BL21, BL21/pOri1 and BL21/pOri2 were analysed using DNA microarray technology. BL21, BL21/pOri1 or BL21/pOri2 strains were cultured at chemostat status and harvested after the cultivation arrived steady status. Keywords: Effects of plasmid DNA on Escherichia coli metabolism
2006-07-07 | GSE5239 | GEO
Project description:Responses of Escherichia coli MG1655/pTrc99a(NOX+) grown at different growth rates in chemostat in M9 + salts NOX: NADH oxygenase converts NADH to NAD. Cells with NOX are able to recycle the excess NADH generated during rapid growth, leading to lesser accumulation of acetate Keywords: different growth rates in parallel
2006-03-08 | GSE4365 | GEO
Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pneumoniae and Streptococcus pyogenes, 5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. This submission contains the results from five Escherichia coli strains (B36, MS14384, MS14385, MS14386, MS14387) grown in either RPMI or pooled human sera. Six replicates of each condition were subjected to shotgun proteomics and label-free MS1-based quantitation.
2021-07-05 | PXD020545 | Pride
Project description:Comparison of Escherichia coli MG1655 and isogenic Qor mutant grown under identical chemostat conditions
2005-12-01 | E-MEXP-245 | biostudies-arrayexpress
Project description:Escherichia coli strain MG1655 was grown in parallel chemostat cultures in GGM. In one chemostat the culture was fed adequate Zn; in the other, measures were taken to eliminate Zn from the chemostat vessel and culture medium. Culture volume (120 ml), temperature (37 oC) and stirring speed (437 rpm) were maintained. Steady state values for pH and OD600 were 6.9 and 0.6, respectively. After 50 hours, samples from the adequate Zn and Zn-limited chemostats were harvested into RNAprotect and total RNA was purified using Qiagen’s RNeasy Mini kit (using the supplier’s protocol) prior to use in microarray analysis. Biological experiments (i.e. a comparison of adequate versus low Zn in chemostat culture) were carried out three times, and a dye swap performed for each experiment, providing two technical repeats for each of the three biological repeats.
2009-05-29 | GSE11894 | GEO
Project description:Escherichia coli strains MG1655 and an isogenic norR::Tn5 mutant were grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.1 h-1. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added at a final concentration of 50 mM to act as a terminal electron acceptor. Cells were grown as above to steady-state, At steady-state, NOC-5 and NOC-7 were added to the chemostat culture and to the nutrient feed at a final concentration of 10 uM of each. Samples were taken after a period of 5 min exposure to NOC for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers. Equal quantities of RNA from Wild type and norR::Tn5 cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values Keywords: Mutant Comparison, stress response, nitric oxide, NorR, chemostat, continuous culture
2006-09-01 | GSE5084 | GEO
Project description:Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.
2016-02-06 | GSE77325 | GEO