Plant
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA421402 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Nanopore sequencing data of rolling-circle amplification (RCA) products performed on hES cells, treated with 2mJ UV-C to induce apoptosis. The experimental conditions were designed to characterize circular DNA forms generated during apoptosis. gDNA from untreated and UV-treated cells are used as controls.
2026-04-30 | E-MTAB-16581 | biostudies-arrayexpress
Project description:We report isoCirc, a long-read sequencing strategy coupled with an integrated computational pipeline to characterize full-length circular RNA (circRNA isoforms) using rolling circle amplification (RCA) followed by long-read sequencing. Applying isoCirc to 12 human tissues, we determined full-length structures and examined tissue specificities of circRNA isoforms in human transcriptomes.
2020-09-12 | GSE141693 | GEO
Project description:Circular RNAs (circRNAs) exhibit extended stability and enhanced,sustained protein expression. Nucleoside modification and rolling circle translation are supposed to reduce the immunogenicity and enhance the translational efficiency of circRNAs. However, it remains challenging to produce encodable circRNAs with modified nucleosides rather than the original nucleosides. Here, we identified a 39-nucleotide Cap-independent Translation Enhancer (CITE) element, termed BBV, which effectively drove the translation of nucleoside-modified RNAs with minimal immunogenicity. Subsequently, we demonstrated that the in vivo-produced circRNA harboring BBV could achieve efficient and sustained rolling circle translation lasting two weeks. Furthermore, we developed an extracellular vesicle-based delivery platform, termed EPM-EABR ASsisted Vesicle Yield (EASY), to deliver circRNAs without introducing viral Gag-Pol proteins. Additionally, we developed a Permuted Intron for Clean CircRNAs (PICC) system to produce scarless circRNAs via in vitro transcription and achieved efficient rolling circle translation driven by BBV. In a murine model, we demonstrated that the PICC-produced circRNA vaccine outperformed the N1mψ-mRNA vaccine in inducing anti-tumor immunity. Importantly, we succeeded to achieve complete substitution with modified nucleosides in circRNAs via Twister ribozyme self-cleaving, dramatically reducing the immunogenicity of circRNAs, but still retaining the ability of rolling circle translation. Collectively, we established a nucleoside-modified circRNA platform that facilitates efficient translation with minimal immunogenicity, offering a safer and more effective platform for applications in vaccine development and disease treatment.
2026-02-28 | GSE303451 | GEO
Project description:These experiments were to investigate changes in gene expression associated with maize competition for light when grown at double normal population density or under 60% shaded conditions as opposed to when maize is grown under normal field conditions. Three biological replicates (collected from separate field plots) comprised of pooled samples of 4 plants from each treatment were hybridized in a rolling circle dye swap hybridization screen.
2008-12-04 | E-GEOD-13768 | biostudies-arrayexpress
Project description:Transcription profiiling of arabidopsis transgenic Rca-T78S comparing Control WT plant (Rca-T78). Rca is Rubisco activase and Threonine78 residue of Rca is phosphorylated only in the dark. However, Serine substituted Rca (T78S) was phosphorylated even in the light. Thus, Rca-T78 or Rca-T78S expressing plants which were exposed light for an hour were harvested to check gene expression pattern
2018-09-17 | GSE117263 | GEO
Project description:Next-Generation Sequencing (NGS) catalyzed breakthroughs across various scientific domains. Illumina's sequencing by synthesis method has long been essential for NGS but emerging technologies like Element Biosciences' sequencing by avidity (AVITI) represent a novel approach. It has been reported that AVITI offers improved signal-to-noise ratios and cost reductions. However, the method relies on rolling circle amplification which can be impacted by polymer size, raising questions about its efficacy sequencing small RNAs (sRNAs) libraries including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and others that are crucial regulators of gene expression and involved in various biological processes. In addition, capturing capped small RNAs (csRNA-seq) has emerged as a powerful method to map active or “nascent” RNA polymerase II transcription initiation in tissues and clinical samples. Finally, we present an accelerated and optimized protocol for small fragment sequencing with AVITI that aligns seamlessly with available sRNA library kits to meet this need.
2024-06-26 | GSE267848 | GEO