Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression

ABSTRACT: This study demonstrates simulated microgravity effects on E. coli K 12 MG1655 when grown on LB medium supplemented with glycerol. The results imply that E. coli readily reprograms itself to combat the multiple stresses imposed due to microgravity. Under these conditions it survives by upregulating oxidative stress protecting genes and simultaneously down regulating the membrane transporters and synthases to maintain cell homeostasis. In this study, a clinostat that mimics microgravity conditions was used to investigate the effects of microgravity on E. coli grown in LB medium supplemented with glycerol to monitor the effects on growth and global gene expression using Affymetrix DNA microarrays.

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

SUBMITTER: kotakonda Arunasri

PROVIDER: E-GEOD-40648 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression

Project description:This study demonstrates simulated microgravity effects on E. coli K 12 MG1655 when grown on LB medium supplemented with glycerol. The results imply that E. coli readily reprograms itself to combat the multiple stresses imposed due to microgravity. Under these conditions it survives by upregulating oxidative stress protecting genes and simultaneously down regulating the membrane transporters and synthases to maintain cell homeostasis.

2012-09-06 | GSE40648 | GEO

action of microgravity on root development-Action of microgravity on root development

Project description:au11-03_gravite - action of microgravity on root development - Action of microgravity on root development - Arabidopsis were grown on horizontal or vertical clinostat for 4, 8 or 12 days. Seedlings on horizontal clinostat were in simulated microgravity and seedlings on vertical clinostat are considered as a control. Comparison was made between plants grown on simulated microgravitry and vertical position. 6 dye-swap - treated vs untreated comparison

2012-07-31 | E-GEOD-39631 | biostudies-arrayexpress

DNA microarray analysis of E.coli K12 MG1655 exposed to prolonged stationary phase

Project description:This study explores the effects of prolonged stationary phase, on whole genome expression of Escherichia coli. In summary these results imply that prolonged stationary phase cells have shown less growth rate compared to fresh cells due to the low abundance of transcripts for translation initiation factor infC, and for all the seven rrn operons of 5S, 16S, 23S ribosomal RNA which further delayed in protein synthesis leading to low biomass in prolonged stationary phase cells. 28 days old E.coli cells were grown in the presence of LB broth and LB broth supplemented with 10% v/v glycerol. RNA was extracted from these samples, cDNA was prepared, fragmented cDNA was labled with labeling reagent and hybridized with Affymetrix E.coli2.0 genome array chips.Data was analysed to get the effect of glycerol on E.coli gene expression

2013-09-12 | E-GEOD-50828 | biostudies-arrayexpress

Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to simulated microgravity based on comparative transcriptomics (2-color)

Project description:In order to gain a better understanding of the effects of Streptomyces coelicolor A3(2) wild type strain exposed to simulated microgravity condition by clinorotation, we constructed a whole genome microarray to screen simulated microgravity sensitive genes using the Agilent eArray 5.0 program. The genechip was custom designed according to the manufacturer’s recommendations (Agilent, 8*15K). The genome sequences were downloaded from: http://www.ncbi.nlm.nih.gov/genome?Db =genome&Cmd = Search&Term = NC_003888, NC_003903.1, NC_003904.1. Each gene was represented by one 60-nt oligonucleotide probe, and 680 genes associated with morphological differentiation and secondary metabolism out of the total 8116 genes were replicated 9 times each. Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 28°C for 144h (6d) under simulated microgravity (by a rotating clinostat) and 1g control conditions respectively. Total RNA was extracted to conduct the microarray hybridization experiments for two color (Cy3/Cy5).

2014-02-01 | E-GEOD-53749 | biostudies-arrayexpress

action of microgravity on root development-Action of microgravity on root development

2012-08-01 | GSE39631 | GEO

Proteomic Analysis of the Effects of Simulated Microgravity in GES-1 Cells

Project description:Microgravity is an ecological factor that affect the environment of the body. In this study, quantitative isobaric labeling (tandem mass tag) methods were used to study the changes in human gastric mucosal cells under simulated microgravity.

2022-03-03 | PXD026675 | Pride

Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites

Project description:This study explores the effects of glycerol, on whole genome expression of Escherichia coli. DNA microarray analysis imply that E. coli in the presence of glycerol generates acidic metabolites to which it adapts by upregulation of genes involved in acid stress and by simultaneously downregulating genes involved in high pH stress. E.coli was grown in the presence and absence of glycerol. RNA was extracted from these samples, cDNA was prepared, fragmented cDNA was labled with labeling reagent and hybridized with Affymetrix E.coli2.0 genome array chips.Data was analysed to get the effect of glycerol on E.coli gene expression

2011-12-09 | E-GEOD-34275 | biostudies-arrayexpress

Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol

Project description:The aim of this study is to investigate the changes of global gene expression in E. coli during a carbon source shift. Expression profiling of an evolved strain of E. coli K12 MG1655 grown in M9 minimal media supplemented with propylene glycol or glycerol.

2012-06-01 | GSE34631 | GEO

Time-resolved transcript, protein and metabolite profiling of Arabidopsis roots in simulated microgravity

Project description:Arabidopsis seedlings were grown for 1 week in Aradishes and then subjected to 5 min to 10 h of simulated microgravity using a 2D clinostat. RNA; proteins and metabolites were extracted and analyzed by RNA.seq and label free quantitative MS.

2022-12-31 | E-MTAB-4873 | biostudies-arrayexpress

Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints

2011-10-22 | GSE33147 | 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