Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression level during L-threonine production

ABSTRACT: The comparative transcriptome profiling of L-threonine producing strain (TH07 strain harboring pBRThrABC) and control W3110 (lacI-deleted) strain harboring pKK223-3 has been analyzed using oligo nucleotide microarray. Keywords: comparative transcriptome analysis (between L-threonine producing strain and the control strain)

ORGANISM(S): Escherichia coli

PROVIDER: GSE9434 | GEO | 2007/10/26

SECONDARY ACCESSION(S): PRJNA103185

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression level during L-threonine production

Project description:The comparative transcriptome profiling of L-threonine producing strain (TH07 strain harboring pBRThrABC) and control W3110 (lacI-deleted) strain harboring pKK223-3 has been analyzed using oligo nucleotide microarray. Keywords: comparative transcriptome analysis (between L-threonine producing strain and the control strain) Samples for transcriptome profiling were taken at the OD600 of 5.13 (TH07 harboring pBRThrABC) and 5.21 (control strain), replicate = 2

2010-05-25 | E-GEOD-9434 | biostudies-arrayexpress

Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (Ribosome profiling)

Project description:To understand the underlying mechanism of YRDC, an enzyme catalysing the formation of N6-threonylcarbamoyladenosine (t6A) on ANN-decoding tRNAs, and the interplay between threonine and YRDC in glioblastoma stem cells (GSCs), we carried out comparative transcriptomic analysis in patient-derived GSC456 with or without YRDC deprivation and with or without threonine restriction (control media, 800 μM threonine; threonine-restricted media, 4 μM). To further investigate the translational regulation of YRDC and threonine in GSCs, we performed ribosome profiling in GSC456 with or without YRDC deprivation and with or without threonine restriction (control media, 800 μM threonine; threonine-restricted media, 4 μM).

2024-01-06 | GSE229672 | GEO

Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (RNA-Seq)

2024-01-06 | GSE229671 | GEO

Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming (tRNA-Seq)

2024-01-06 | GSE245043 | GEO

Anaerobic cysteine catabolism, sulfide production, and their regulation in Escherichia coli and Salmonella enterica

Project description:Gene expression in E coli W3110 strains with either ybaO over-expression (W3110/pcutR) or ybaO deletion (W3110/ΔcutR) were measured with cysteine challenge.

2017-06-13 | GSE90066 | GEO

The effects of artificial tethering of chromosomes to the nuclear periphery using LacI/lap2b anchorage constructs, part 2

Project description:Experiment: analysis of gene expression changes between J21.c3 (non tethered) vs J21.c3 lacI-lap2b (lap2b-lacI tethered) that both possess a Chr11 128mer LacO integrant Keywords: comparative hybridization to access expression profiles between tethered and non tethred cells.

2008-03-04 | GSE10699 | GEO

Comparative Phenotypic, Proteomic, and Phosphoproteomic Analysis Reveals Different Roles of Serine/Threonine Phosphatase and Kinase in the Growth, Cell Division, and Pathogenicity of Streptococcus suis

Project description:To investigate the influence of STP and STK on protein expression in S. suis, we performed a comparative proteomics analysis with the WT, Δstp, and Δstk strains using liquid chromatography mass spectrometry/mass spectrometry (LC-MS/MS).STK and STP are serine/threonine kinases and phosphatases, respectively. Therefore, we next analyzed the changes in the abundance of serine/threonine phosphorylated proteins in Δstp and Δstk compared with the WT strain.

2021-11-30 | PXD029994 | Pride

Time-course transcriptome analysis of non-antibiotics producer and actinorhodin over-producing Streptomyces coelicolor strain

Project description:To identify unique gene expression in higher antibiotics producing Streptomyces coelicolor strain, non-producer M1146 and the derivative strain M1146+ACT (M1146 with actinorhodin biosynthetic genes cluster) was choosen for comparative transcriptome analysis. The genes with different gene expression might be key genes important for antibiotics production.

2020-11-27 | GSE155796 | GEO

RNAseq of engineered S. cerevisiae strains for isobutanol production

Project description:Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced (NADPH-dependent) or redox-balanced (NADH-dependent) ketoacid reductoisomerase enzyme. We then conducted transcriptomic, proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains. Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes. Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version, albeit at low overall pathway flux. Functional genomic analyses indicated that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters, which are required cofactors for the dihydroxyacid dehydratase enzyme. We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation, thereby increasing cellular iron levels. The resulting isobutanol titer of the fra2-null strain harboring a cytosolic localized isobutanol pathway outperformed the strain with the mitochondrial localized pathway by 1.3-fold, demonstrating that both localizations can support flux to isobutanol.

2021-10-22 | GSE186126 | GEO

Whole genome ChIP-seq of histone H3 threonine 11 phosphorylation in Saccharomyces cerevisiae

Project description:We used ChIP-seq to determine the whole-genome enrichment of histone H3 threonine 11 phosphorylation (H3 T11ph) during Saccharomyces cerevisiae meiosis. S. cerevisiae SK1 cells were synchronized for meiotic entry and 3 and 4 hour meiotic samples were obtained. As H3 T11ph is dependent on the formation of meiotic double strand breaks (DSBs), a negative control ChIP-seq sample was obtained from a strain lacking DSBs (spo11-yf). Concurrently, ChIP-seq was carried out for histone H3 as a control for comparision.

2017-06-28 | GSE100564 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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