Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LIX11 vs H37Rv under Log vs stationary phase growth

ABSTRACT: Transcription analysis of ΔpknK mutant (LIX11) versus wild type H37Rv during logarithmic and stationary phase growth. This will elucidate the genes regulated by PknK during transition from logarithmic growth to stationary phase growth.

ORGANISM(S): Mycobacterium tuberculosis H37Rv

PROVIDER: GSE37823 | GEO | 2012/06/02

SECONDARY ACCESSION(S): PRJNA163615

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

LIX11 vs H37Rv under Log vs stationary phase growth

Project description:Transcription analysis of M-NM-^TpknK mutant (LIX11) versus wild type H37Rv during logarithmic and stationary phase growth. This will elucidate the genes regulated by PknK during transition from logarithmic growth to stationary phase growth. Two color Experiment,Organism: Mycobacterium tuberculosis, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-26323 and AMADID-23057

2012-06-01 | E-GEOD-37823 | biostudies-arrayexpress

Listeria monocytogenes Cold Regulon in Log- and Stationary-Phase cells

Project description:As the foodborne pathogen Listeria monocytogenes has the ability to grow at refrigeration temperatures, whole-genome microarray experiments were performed using L. monocytogenes strain 10403S to define the cold stress regulon and to identify genes differentially expressed during growth at 4°C and 37°C. Microarray analysis using a stringent cutoff (adjusted p<0.001; fold-change >2.0) revealed 105 and 170 genes that showed higher transcript levels in logarithmic- and stationary-phase cells, respectively, at 4°C (compared to cells at 37°C). A total of 74 and 102 genes showed lower transcript levels in logarithmic- and stationary-phase cells grown at 4°C, respectively. Genes upregulated at 4°C during both stationary- and log-phase included those encoding a two-component response regulator (lmo0287), a cold shock protein (cspL), and two RNA helicases (lmo0866 and lmo1722), whereas genes encoding selected virulence factors and heat shock proteins were downregulated at 4°C. Selected genes that were upregulated at 4°C during both stationary- and log-phase were confirmed by quantitative reverse transcriptase PCR. Our data show (i) a large number of L. monocytogenes genes are differentially expressed at 4 and 37°C with a larger number of genes showing higher transcript level at 4°C than genes showing lower transcript levels at 4°C; (ii) L. monocytogenes genes upregulated at 4°C include a number of genes and operons with previously reported or plausible roles in cold adaptation; and (iii) L. monocytogenes genes downregulated at 4°C include a number of virulence and virulence-associated genes as well as some heat shock genes. Keywords: Listeria monocytogenes, cold regulon, temperature

2007-08-31 | GSE7465 | GEO

Xbp1 binding during log phase and stationary phase.

Project description:To determine where Xbp1 binds to chromatin during log phase and stationary phase, we performed ChIP-seq.

2022-08-17 | GSE210933 | GEO

Tup1 binding during log phase, diauxic shift, and stationary phase.

Project description:To determine where Tup1 binds to chromatin during log phase, diauxic shift and stationary phase, we performed ChIP-seq.

2022-08-17 | GSE210932 | GEO

Pairwise comparison stationary phase vs mid-log

Project description:A pairwise comparison was performed between stationary phase specific samples and mid-log samples using four replicates and dye-swaps

2005-04-15 | E-UMCU-13 | biostudies-arrayexpress

Acinetobacter oleivorans DR1 : WT stationary phase vs. aqsR mutant stationary phase

Project description:Transcriptional profiling of A. oleivorans DR1 cells comparing wild type stationary phase cells with aqsR mutant stationary phase cells.

2013-02-16 | GSE44347 | GEO

Mycobacterium tuberculosis H37Rv

Project description:LIX11 vs H37Rv under Log vs stationary phase growth

| PRJNA163615 | ENA

LIX75 vs H37Rv under Log phase growth (± 5 mM Nitrate), and during hypoxic growth (48 h)

Project description:Transcription analysis of ΔnarL mutant (LIX75) versus wild type H37Rv during aerobic growth in absence or presence of 5 mM Nitrate, and during hypoxic growth. This will elucidate the regulatory role of NarL response regulator duirng aerobic growth in absence of presence of exogenous nitrate supplemen and during hypoxic growth conditions and help identify genes that require NarL for expression under the three experimental conditions.

2015-02-09 | GSE59063 | GEO

Transcription profiling of three Bordetella bronchiseptica strains at three distinct phases of growth: mid-log phase, late-log phase, and late-stationary phase

Project description:Microarray analysis was performed to determine if the growth-dependent gene expression changes occurred on a global scale for B. bronchiseptica strains RB50, RB53, and RB54. For this analysis cDNA representing three distinct phases of growth: mid-log phase (15H), late-log phase (24H), and late-stationary phase (48H) were directly compared.

2009-07-01 | E-MEXP-2015 | biostudies-arrayexpress

Analysis of Growth Phases of Enterotoxigenic Escherichia coli Reveals a Distinct Transition Phase before Entry into Early Stationary Phase with Shifts in Tryptophan, Fucose, and Putrescine Metabolism and Degradation of Neurotransmitter Precursors

Project description:Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and adults in endemic areas. Gene regulation of ETEC during growth in vitro and in vivo needs to be further evaluated, and here we describe the full transcriptome and metabolome of ETEC during growth from mid-logarithmic growth to early stationary phase in rich medium (LB medium). We identified specific genes and pathways subjected to rapid transient alterations in gene expression and metabolite production during the transition from logarithmic to stationary growth. The transient phase was found to be different from the subsequent induction of early stationary phase-induced genes. The transient phase was characterized by the repression of genes and metabolites involved in organic substance transport. Genes involved in fucose and putrescine metabolism were upregulated, and genes involved in iron transport were repressed. Expression of toxins and colonization factors were not changed, suggesting retained virulence from mid-logarithmic to the start of the stationary phase. Metabolomic analyses showed that the transient phase was characterized by a drop of intracellular amino acids, e.g., L-tyrosine, L-tryptophan, L-phenylalanine, L-leucine and L-glutamic acid, followed by increased levels at induction of stationary phase. A pathway enrichment analysis of the entire combined transcriptome and metabolome revealed that significant pathways during progression from logarithmic to early stationary phase are involved in the degradation of neurotransmitters aminobutyrate (GABA) and precursors of 5-hydroxytryptamine (serotonin). This work provides a comprehensive framework for further studies on transcriptional and metabolic regulation in pathogenic E. coli.

2022-07-15 | MTBLS3540 | MetaboLights

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