Ontology highlight
ABSTRACT:
PROVIDER: PRJNA800589 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We isolated and sequenced mRNA from Streptomyces venezuelae grown on solid medium that promotes exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time.
2021-10-22 | GSE186259 | GEO
Project description:This project aims to discover novel bioactive compounds from Streptomyces isolated from the rhizosphere from wild medicinal plants from Hamedan province, Iran. Proteomics is used to assist in discovery and characterization of the compounds. Streptomyces isolates are grown on ISP-4 medium for three days, proteins were extracted and analysed by shotgun proteomics.
2024-01-04 | PXD041994 | Pride
Project description:To investigate the function of organic nitrogen on clavulanic acid biosynthesis in Streptomyces clavuligerus, we established F613-1 strain cells cultured in MH fermentation medium and ML fermentation medium. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different medium at three time points.
2022-08-25 | GSE211765 | GEO
Project description:In order to define the impact of phosphate (Pi) availability on cellular metabolism the project aimed to perform a comparative analysis of the proteomes of two Streptomyces strains with different abilities to produce antibiotics, S. coelicolor and S. lividans as well as of the pptA mutant of S. lividans, grown low (1mM) and high (5mM) phosphate (Pi) availability conditions. Interestingly, in contrast to most Streptomyces species, S. coelicolor produces more antibiotics in Pi proficiency than in Pi limitation, S. lividans does not produce antibiotics in any Pi conditions and the pptA mutant produces antibiotics only in Pi limitation. This in-depth proteomic comparison of three Streptomyces strains (S. coelicolor, S. lividans wt and pptA mutant), in different growth conditions (time and Pi concentration in the medium) was performed on four biological replicates. Protein abundance changes were determined using two label-free mass spectrometry based-quantification methods: spectral count (SC) and MS1 ion intensities named XIC (for eXtracted Ion Current). Our proteomic data reveal for the first time, the impact of Pi availability on the abundance of approximately 4000 proteins of these Streptomyces strains with different abilities to produce antibiotics. The most striking feature differentiating these strains was the much higher abundance of enzymes of the respiratory chain in both phosphate conditions in S. coelicolor compared to the S. lividans strains.
2022-02-04 | PXD029263 | Pride
Project description:We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote different growth behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.
2023-08-19 | GSE240807 | GEO
Project description:During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix GeneChip and a high-resolution time-series of fermenter-grown samples. This time series was conducted using medium leading to glutamate depletion and the cultivation conditions as published in Nieselt et al. BMC Genomics 2010, performed with the Streptomyces coelicolor wild type strain M145E.
2011-12-31 | GSE30569 | GEO
Project description:We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.
2021-07-30 | GSE181041 | GEO
Project description:Here we compare RNA expression profiles of colorectal cancer organoids grown in four different conditions, namely standard organoids medium, minimal medium without growth factors or with normal or cancer associated fibroblasts. We found majorly different expression profiles between conditions and more heterogeneous tumor cell population in organoids grown with fibroblasts.
2023-02-01 | GSE198697 | GEO
Project description:The terminal compartments of Streptomyces are less prone to transcription than the rest of the chromosome. Indeed, the expression of the highly variable regions enriched in those compartments is generally conditional and often requires an empirical approach to characterize the inducing conditions. For instance, in the context of identifying adequate antibiotic production conditions, an OSMAC (“One Strain Many Compounds”) approach is frequently implemented, based on strain cultivation in different environmental conditions (composition of the medium, growth time, temperature, co-cultures, etc.). Likewise, to find the expression conditions of a complete prophage of Streptomyces ambofaciens ATCC 23877 (named 'Samy' phage/prophage), we conducted a similar approach by analyzing the transcriptomes in five solid media (HT, SAF, ONA, MMM, MMM+NAG). The terminal compartments of Streptomyces are less prone to transcription than the rest of the chromosome. Indeed, the expression of the highly variable regions enriched in those compartments is generally conditional and often requires an empirical approach to characterize the inducing conditions. For instance, in the context of identifying adequate antibiotic production conditions, an OSMAC (“One Strain Many Compounds”) approach is frequently implemented, based on strain cultivation in different environmental conditions (composition of the medium, growth time, temperature, co-cultures, etc.). Likewise, to find the expression conditions of a complete prophage of Streptomyces ambofaciens ATCC 23877 (named 'Samy' phage/prophage), we conducted a similar approach by analyzing the transcriptomes in five solid media (HT, SAF, ONA, MMM, MMM+NAG).
2023-07-01 | GSE232795 | GEO
Project description:Investigation of whole genome gene expression level changes in Streptomyces sp. SirexAA-E (ActE) when grown on different carbon sources. The results of this study demonstrate that ActE upregulates a small number of genes specific for the utilization of the avaliable carbon source. Cellulolytic Streptomyces sp. SirexAA-E (ActE), isolated from the pinewood-boring wasp Sirex noctilio, has a genome enriched for biomass utilization. The secreted proteomes obtained from growth on pure polysaccharides catalyzed hydrolysis of cellulose, mannan, and xylan with specific activities comparable to Spezyme CP, a commercial cellulase preparation. During reaction of an ActE secretome with cellulose, reducing sugar release was markedly stimulated in the presence of O2. ActE also expresses and secretes an expanded repertoire of enzymes during growth on natural and pre-treated biomass. These results indicate a new microbial contribution to biomass utilization that is widely distributed in natural environments by insects Streptomyces sp. ActE was grown in minimal medium supplimented with 0.5% carbon source (glucose, sigmacell-20, xylan, chitin, cellobiose, or AFEX). Cells were grown for 7 days and total RNA was extracted from the cell pellet. At least 3 biological replicates were performed for each carbon source (glucose, 3; sigmacell, 3; xylan, 5; chitin, 3; cellobiose 3; AFEX 3). Each biological replicate contained 3 technical replicates. The complete dataset were RMA Background Corrected, quantile normalized, the RMA algorithm was utilized by DNAStar ArrayStar.
2013-12-31 | E-GEOD-31748 | biostudies-arrayexpress