Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Helicobacter pylori N6 wild-type and HP1021 deletion mutant under microaerophilic and aerobic conditions (optimal growth and oxidative stress conditions, respectively)

ABSTRACT: We performed transcriptome (RNA-seq) analyses for Helicobacter pylori N6 wild-type (WT) and HP1021 deletion mutant (ΔHP1021::aphA-3) under oxidative stress and optimal microaerobic growth conditions. The expression of 411 genes was affected by oxidative stress in stressed wild-type cells (WTS) compared to non-stressed cells (WT). Interestingly, ΔHP1021 did not respond to oxidative stress. A comparison of genes expressed in the ΔHP1021 and WT strains under optimal growth conditions revealed 191 differently expressed genes. Moreover, transcriptional changes and overall final protein levels correlated across multiple genes. The data were validated through RT-qPCR and phenotype experiments for selected processes.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Helicobacter pylori

SUBMITTER: Mateusz Noszka

PROVIDER: E-MTAB-13025 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of Campylobacter jejuni 11168 wild-type and Cj1608 deletion mutant under microaerophilic and paraquat stress conditions

Project description:We performed transcriptome (RNA-seq) analyses for Campylobacter jejuni 11168 wild-type (WT) and Cj1608 deletion mutant (ΔCj1608::aphA-3) under oxidative stress and optimal microaerobic growth conditions. The expression of 231 genes was affected by oxidative stress in stressed wild-type cells (WTS) compared to non-stressed cells (WT). A comparison of genes expressed in the ΔCj1608 and WT strains under optimal growth conditions revealed 380 differently expressed genes. Moreover, transcriptional changes and overall final protein levels correlated across multiple genes. The data were validated through RT-qPCR and phenotype experiments for selected processes.

2024-06-14 | E-MTAB-13650 | biostudies-arrayexpress

RNA-seq of Arcobacter butzleri RM4018 wild-type and Abu0127 deletion mutant under microaerophilic and paraquat stress conditions

Project description:We performed transcriptome (RNA-seq) analyses for Arcobacter butzleri RM4018 wild-type (WT) and Abu0127 deletion mutant (ΔAbu0127::aphA-3) under oxidative stress and optimal microaerobic growth conditions. The expression of 290 genes was affected by oxidative stress in stressed wild-type cells (WTS) compared to non-stressed cells (WT). A comparison of genes expressed in the ΔAbu0127 and WT strains under optimal growth conditions revealed 779 differently expressed genes. Moreover, transcriptional changes and overall final protein levels correlated across multiple genes. The data were validated through RT-qPCR and phenotype experiments for selected processes.

2024-06-14 | E-MTAB-13649 | biostudies-arrayexpress

Regulation of filamentation in the human fungal pathogen Candida tropicalis

Project description:The yeast-filament transition is essential for the virulence of a variety of fungi that are pathogenic to humans. N-acetylglucosamine (GlcNAc), a ubiquitous molecule in both the environment and host, is one of the most potent inducers of filamentation in Candida albicans and thermally dimorphic fungi such as Histoplasma capsulatum and Blastomyces dermatitidis. However, GlcNAc suppresses rather than promotes filamentation in Candida tropicalis, a fungal species that is closely related to C. albicans. Furthermore, we discover that glucose induces filamentous growth in C. tropicalis. Mutation and overexpression assays demonstrate that the conserved cAMP signaling pathway plays a central role in the regulation of filamentation in C. tropicalis. Activation of this pathway promotes filamentation in C. tropicalis, while inactivation of this pathway results in a serious growth defect in filamentation. By screening an overexpression library of 154 transcription factors, we have identified approximately 40 regulators of filamentous growth in C. tropicalis. Although most of the regulators (e.g., Tec1, Gat2, Nrg1, Sfl1, Sfl2, and Ash1) demonstrate a conserved role in the regulation of filamentation, similar to their homologs in C. albicans or S. cerevisiae, some of them are specific to C. tropicalis. For example, Czf1 and Efh1 repress filamentation, while Wor1, Zcf3, and Hcm1 promote filamentation in C. tropicalis. Bcr1, Aaf1, and Csr1 play a specific role in the process of GlcNAc-regulated filamentation. Our findings indicate that multiple interconnected signaling pathways are involved in the regulation of filamentation in C. tropicalis. These mechanisms have conserved and divergent features among different Candida species. Total RNA profiles of cells grown in Lee's glucose or Lee's GlcNAc medium.

2016-07-01 | E-GEOD-73340 | biostudies-arrayexpress

Discovery of a "White-Gray-Opaque" Tristable Phenotypic Switching System in Candida Albicans: Roles of Non-Genetic Diversity in Host Adaption

Project description:The capacity of the commensal yeast Candida albicans to grow in several forms, referred to as phenotypic plasticity, is critical for its survival, and abilities to thrive and cause infection in the human host. In this study, we report a novel phenotype of C. albicans, referred as the “gray” phenotype. The gray cell type, together with the previously discovered “white” and “opaque” cell types, forms a tristable phenotypic switching system. The three phenotypes differ in cellular and colony appearance, global transcriptional profiles, secreted aspartyl proteinase (Sap) activities and virulence in different infection models. The addition of the gray cell type to the phenotypic transition systems may enhance fitness and confers an adaptive advantage for C. albicans in the host. We further demonstrate that two key regulators of white-opaque switching, Wor1 and Efg1, are not required for maintenance of the gray phenotype, suggesting that a different regulatory circuitry may be involved in the regulation of gray cell formation. Our study provides an example of multiple stable and heritable switching systems, indicating that the regulation of morphological forms to adapt to environmental changes could be much more elaborate than previously thought. total RNA profiles of 24h old white, gray and opaque cell types

2014-06-30 | E-GEOD-53671 | biostudies-arrayexpress

White Cells Facilitate Opposite- and Same-Sex Mating of Opaque Cells in Candida albicans

Project description:Modes of sexual reproduction in eukaryotic organisms are highly diversified. The human fungal pathogen Candida albicans undergoes a phenotypic switch from the white to the opaque phase in order to become mating-competent. In this study, we report that functionally and morphologically differentiated white and opaque cells show a coordinating behavior in the process of mating. Although white cells are mating-incompetent, they are induced to produce sexual pheromones when treated with opposite pheromones or interacted with opaque cells of an opposite mating type. In a co-culture system, pheromones released by white cells induce opaque cells to form mating projections and thus facilitate both opposite- and same-sex mating of opaque cells. Deletion of genes encoding the pheromone precursor proteins and inactivation of the pheromone response signaling pathway (Ste2-MAPK-Cph1) impair the promoting role of white cells (MTLa) in sexual mating of opaque cells. White and opaque cells communicate via a paracrine pheromone signaling and thus create an environment conducive to sexual mating. This coordination behavior of the two different cell types may be a trade-off strategy between sexual and asexual lifestyles in C. albicans. total RNA profiles of white cell treated with pheromone

2014-10-23 | E-GEOD-56039 | biostudies-arrayexpress

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha [gene expression]

Project description:Lamins are components of the peripheral nuclear lamina and interact with heterochromatic genomic regions, termed lamina-associated domains (LADs). In contrast to lamin B1, lamin A/C also localizes throughout the nucleus, where it associates with the chromatin-binding protein lamina-associated polypeptide (LAP) 2alpha. Here we show lamin A/C also interacts with euchromatin, as determined by chromatin immunoprecipitation analyses of eu- and heterochromatin-enriched samples. By way of contrast, lamin B1 was only found associated with heterochromatin. Euchromatic regions occupied by lamin A/C overlap with those bound by LAP2alpha, the depletion of which shifts binding of lamin A/C towards more heterochromatic regions. These alterations in lamin A/C chromatin interaction affect epigenetic histone marks in euchromatin without significantly affecting gene expression, while loss of lamin A/C in heterochromatic regions increased gene expression. Our data show a novel role of nucleoplasmic lamin A/C and LAP2alpha in regulating euchromatin. Examination of LaminA, LaminB and Lap2a DNA binding in Lap2alpha +/+ and Lap2a -/- cells and according changes in Histone modifications and gene expression

2016-01-19 | E-GEOD-70148 | biostudies-arrayexpress

White-Opaque Switching in Natural MTLa/alpha Isolates of Candida albicans: Evolutionary Implications for Roles in Host Adaptation, Pathogenesis and Sex

Project description:The discovery of white-opaque switching in natural MTLa/alpha isolates of Candida albicans sheds new light on the evolution of phenotypic plasticity and host adaptation. Comparing gene expression of white and opaque cells of a MTL a/alpha strain

2013-04-01 | E-GEOD-43938 | biostudies-arrayexpress

siRNA knockdown of GALNT1 in hepatocellular carcinoma HA22T and PLC5 cells

Project description:To determine the whole genome profile of GALNT1 silenced HA22T and PLC5 cells HA22T and PLC5 cells were transfected with non-targeting and GALNT1 specific siRNA with Lipofectamine RNAiMAX for 48 hours and extracted for total RNA

2015-01-03 | E-GEOD-64628 | biostudies-arrayexpress

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-01-19 | E-GEOD-70149 | biostudies-arrayexpress

Global transcript levels during growth of Streptomyces venezuelae wild-type strain

Project description:Transcript levels quantified after 10, 15, and 20 hours of gtowth in liquid rich MYM medium

2023-12-24 | E-MTAB-13607 | biostudies-arrayexpress