Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Streptomyces coelicolor hupA and hupS deletion strain

ABSTRACT: HupA and HupS are nucleoid associated proteins, homologic to E. coli HU protein. Their binding to DNA changes chromosome structure, protects DNA from damage and influences gene expression. The goal of RNA-seq experiment was to determine HupA and HupS regulons during growth in liquid medium. Dataset contains four strains (hupA, hupS, hupAhupS deletion mutants and wild type), two time points (exponential and stationary growth) and two growth conditions (standard media and osmotic stress).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Streptomyces coelicolor

SUBMITTER: Agnieszka Strzałka

PROVIDER: E-MTAB-13846 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Project description: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.

2023-09-23 | E-MTAB-13025 | 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

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

Age-dependent RGS5 loss in pericytes induces cardiac dysfunction and fibrosis in the heart (Bulk RNA-SEQ)

Project description:Background. Ageing is one of the main risk factors of cardiovascular disease. Pericytes are capillary-associated mural cells involved in the maintenance and stability of the vascular network. In the heart, the consequences of ageing on cardiac pericytes are unknown. Methods. In this study, we have combined single nucleus RNA sequencing and histological analysis to determine the effects of ageing on cardiac pericytes. Furthermore, we have conducted in vivo and in vitro analysis of RGS5 loss of function and finally have perfomed pericytes-fibroblasts co-culture studies to understand the effect of RGS5 loss of function in pericytes on the neighbouring fibroblasts. Results. We showed that ageing reduces the pericyte area and coverage. Single nucleus RNA sequencing analysis further revealed that the expression of the Regulator of G protein signalling 5 (Rgs5) is reduced in old cardiac pericytes. In vivo and in vitro studies showed that the deletion of RGS5 induces morphological changes and a pro-fibrotic gene expression signature characterized by the expression of different extracellular matrix components and growth factors like TGFB2 and PDGFB in pericytes. Indeed, the culture of fibroblasts with the supernatant of RGS5 deficient pericytes induced their activation characterized by the increased expression of α smooth muscle actin in a TFGβ2 dependent mechanism. Conclusions. Our results identify RGS5 as a crucial regulator of pericyte function during cardiac ageing. The deletion of RGS5 causes cardiac dysfunction and induces myocardial fibrosis, one of the hallmarks of cardiac ageing.

2024-03-13 | E-MTAB-13833 | biostudies-arrayexpress

Global gene transcription analysis in Streptomyces coelicolor strains with modification of satKR genes.

Project description:We addressed the transcriptional changes in strains with mutations of satKR (sco3390-3389) genes to elucidate which genes are engaged in restoration of sporulation in non-sporulating Streptomyces coelicolor PS04 strain. Our experiments show that SatR can regulate growth and spore formation in Streptomyces and its activity is independent to DNA supercoiling.

2021-08-21 | E-MTAB-10835 | biostudies-arrayexpress

ATAC-seq of human (Homo sapiens) and cynomolgus macaque (Macaca fascicularis) iPSC and iPSC-derived NPC cell lines

Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.

2023-10-25 | E-MTAB-13373 | biostudies-arrayexpress

The nucleoid-associated protein HU controls three regulons that coordinate virulence and general physiology in Salmonella enterica serovar Typhimurium

Project description:The regulon of genes controlled by the HU nucleoid-associated proteins was examined in Salmonella enterica serovar Typhimurium (S. Typhimurium). DNA microarrays were used to detect the effect on the bacterial transcriptome of knockout mutations in the hupA, the hupB and in both the hupA and hupB genes. Distinct but overlapping patterns of gene expression were detected in the transcriptome at each time point for each of the three mutants, pointing to the existence of not one but three regulons of genes controlled by the HU proteins. Mutations in the hup genes altered the expression of regulatory and structural genes in both the SPI1 and the SPI2 pathogenicity islands. The hupA hupB double mutant was found to be defective in invasion of CACO2 and CHO epithelial cell lines and in its ability to survive in J774A.1 macrophage-like cells. The double mutant also had defective swarming activity and had a competitive fitness disadvantage compared to the wild type. In contrast, inactivation of just the hupB gene resulted in increased fitness and correlated with the up-regulation of members of the RpoS regulon in exponential phase cultures. Elimination of both the hupA and hupB genes resulted in strong down-regulation of the genes coding for the integration host factor, IHF, at all three time points. The effect of hupA and hupB single-deletions and hupA and hupB double-deletion on S. Typhimurium gene expression during growth in LB was analysed at 3 different time points (1, 4 and 6 hours post-inoculation). Between two and three biological replicates, as well as technical replicates, were performed for each mutant and time point. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

2011-03-22 | E-GEOD-22860 | biostudies-arrayexpress

RNAseq analysis of Campylobacter jejuni's response to glutamine addition in growth media

Project description:Campylobacter jejuni is a human pathogen which causes campylobacteriosis, one of the most widespread zoonotic enteric diseases worldwide. Growth of Campylobacter can be improved through the addition of glutamine to media which serves as the nitrogen source. RNAseq was used to identify the transcriptomic response of Campylobacter jejuni when the nitrogen source was switched from serine (poor growth) to glutamine (good growth) in chemostat cultures.

2022-12-01 | E-MTAB-11495 | biostudies-arrayexpress

The nucleoid-associated protein HU controls three regulons that coordinate virulence and general physiology in Salmonella enterica serovar Typhimurium

2011-03-22 | GSE22860 | GEO

The impact of cobB1 or cobB2 gene deletions on global transcript levels in Streptomyces venezuelae

Project description:Transcript levels quantified after 10 (vegetative) and 20 (spores maturation) hours of growth in liquid rich MYM medium

2024-04-01 | E-MTAB-13911 | biostudies-arrayexpress