Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression Profiling E. Coli Evolved on Glucose Minimal Media

ABSTRACT: mRNA sequencing was performed on E. coli evolved at 37C on M9 Minimal Media with Glucose Growth of evolved E. coli was characterized under the same conditions as the evolution and compared to the wild type parent strain

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

SUBMITTER: Bernhard Palsson

PROVIDER: E-GEOD-61327 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium.

LaCroix Ryan A RA Sandberg Troy E TE O'Brien Edward J EJ Utrilla Jose J Ebrahim Ali A Guzman Gabriela I GI Szubin Richard R Palsson Bernhard O BO Feist Adam M AM

Applied and environmental microbiology 20141010 1

Adaptive laboratory evolution (ALE) has emerged as an effective tool for scientific discovery and addressing biotechnological needs. Much of ALE's utility is derived from reproducibly obtained fitness increases. Identifying causal genetic changes and their combinatorial effects is challenging and time-consuming. Understanding how these genetic changes enable increased fitness can be difficult. A series of approaches that address these challenges was developed and demonstrated using Escherichia c ...[more]

PMID: 25304508

Similar Datasets

Expression Profiling E. Coli Evolved on Glucose Minimal Media

Project description:mRNA sequencing was performed on E. coli evolved at 37C on M9 Minimal Media with Glucose

2014-12-03 | GSE61327 | GEO

Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide. Data for wild type controls are GSM389302, GSM389303, and GSM389304.

2014-02-05 | E-GEOD-46543 | 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

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

2012-05-31 | E-GEOD-34631 | biostudies-arrayexpress

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

Project description:Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/without heatshock in 42oC. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes with 50-bp length that are spaced 25 bp apart across the E. coli genome (NimbleGen). Experiments were performed with three biological replicates.

2013-06-20 | E-GEOD-42675 | biostudies-arrayexpress

Growth in minimal media with maltose

Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% maltose Keywords: Logical Set

2006-05-20 | GSE4876 | GEO

Growth in minimal media with lactate

Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% lactate versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% lactate Keywords: Logical Set

2006-05-20 | GSE4875 | GEO

Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose

2014-02-05 | GSE46543 | GEO

DNA-seq of E. coli BL21 (DE3) Evolved in High pH (pH = 9) Terrific Broth Media

Project description:Whole genome sequencing was performed on E. coli BL21 (DE3) evolved at 25°C in pH 9 terrific broth media buffered with Tris-HCl (pH 9). The evolved E. coli was characterized and compared to the parent strain.

2023-10-31 | E-MTAB-12334 | biostudies-arrayexpress

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]

Project description:The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons are comprised of 45 genes in 31 transcription units (TUs), significantly expanding the current knowledge of the GadEWX regulatory network. We demonstrate that GadEWX directly and coherently regulate several proton efflux/influx and generating/consuming enzymes with pairs of negative-feedback loops to maintain pH homeostasis by controlling proton flow. In addition, GadEWX regulate genes with assorted functions including molecular chaperones, acid resistance, stress response, and other regulatory activities. These results present a comprehensive understating on how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress. A total of eight samples were analyzed. WT and gadEWX mutant cells were cultured in M9 glucose minimal media at pH 5.5 with biological duplicates.

2015-08-11 | E-GEOD-66481 | biostudies-arrayexpress

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