Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1279650 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Type I polyketide synthases (T1PKSs) hold an enormous potential as a rational production platform for the biosynthesis of speciality chemicals. However, despite the great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression in Corynebacterium glutamicum, Escherichia coli, and Pseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enables the production of an unnatural polyketide in each of the hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables. Here, we not only highlight the significance of codon optimization but also establish the groundwork for high-throughput assembly and characterization of PKS pathways in alternative hosts.
2023-09-01 | PXD042749 | Pride
Project description:We report the application of next-generation sequencing technology for high-throughput profiling of H3K27ac and transcriptome analysis in pancreatic islets derived from C57Bl/6 mice fed a high-fat diet. We find genomic regions showing change in acetylation of histone H3K27 in response to long-term (26 weeks) HFD feeding, which was significantly associated with differential gene expression. Furthermore, increased H3K27ac showed a distinctive genomic distribution surrounding proximal-promoter regions. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cells under various environments.
2018-10-02 | E-MTAB-6719 | biostudies-arrayexpress
Project description:Bacteriophages are highly abundant viruses of bacteria. The major role of phages in microbial ecology to shape bacterial communities and their emerging medical potential as antibacterial agents have triggered a rebirth of phage research. It is of particular interest to understand the molecular mechanisms by which phages gain control over their host. Omics technologies such as next-generation sequencing and protein-profiling technologies can provide novel insights into transcriptional and translational events occurring during the infection process. Thereby, the temporal organization of the transcriptome and proteome of the phage and their bacterial hosts can be monitored. In this study, we performed next-generation sequencing and proteomics to study the transcriptome and proteome of the T4 phage and its host during the infection in a time-resolved manner. Our data shows the temporally resolved appearance of bacteriophage T4 transcripts and proteins, confirming previously described subgrouping of T4 gene products into early, middle and late infection phases. We observe specific early transcripts giving rise to middle or late proteins indicating the existence of previously not reported post-transcriptional regulatory mechanisms controlling the translation of T4 mRNAs. Moreover, we investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying degradation of E. coli transcripts and preservation of the host proteome. This study provides the first comprehensive insights into the transcriptomic and proteomic takeover by the bacteriophage T4, exemplifying the power and value of high-throughput technologies to simultaneously characterize multiple gene expression events. Moreover, we created a user-friendly application available to the entire scientific community to access gene expression patterns for their host and phage genes of interest.
2022-09-19 | PXD035873 | Pride
Project description:We report the application of next-generation sequencing technology for high-throughput profiling of H3K27ac and transcriptome analysis in pancreatic islets derived from C57Bl/6 mice fed a high-fat diet. We find genomic regions showing change in acetylation of histone H3K27 in response to long-term HFD feeding, which was significantly associated with differential gene expression. Furthermore, increased H3K27ac showed a distinctive genomic distribution surrounding proximal-promoter regions. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cells under various environments.
2018-10-02 | E-MTAB-6718 | biostudies-arrayexpress
Project description:Systematic evaluation of conditional gene essentiality changes across 4 yeast strains
| PRJNA507593 | ENA
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in human monocyte devried DCs. By obtaining about 15 million mapped reads for each sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of human monocytes and monocyte-derived DCs. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
2016-11-19 | GSE52510 | GEO
Project description:Small RNA libraries from N. caninum tachyzoites were analyzed using a high-throughput RNA sequencing technology combined with systematic bioinformatics analysis.
2017-11-20 | GSE107118 | GEO
Project description:Characterization of Coronavirus genomes isolated from diverse animal hosts in the wild.
| PRJNA32225 | ENA
Project description:Functional characterization of the transcriptome requires tools for the systematic investigation of RNA post-transcriptional modifications. 2’-O-Methylation of the ribose moiety is one of the most abundant post-transcriptional modifications of the RNA. We describe here a high-throughput method that enables fast and accurate mapping at single-base resolution, and quantitation, of 2’-OMe modified residues. Our approach expands the actual repertoire of methods for transcriptome-wide mapping of RNA post-transcriptional modifications.
2016-09-13 | GSE73065 | GEO