Ontology highlight
ABSTRACT:
PROVIDER: PRJNA862902 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20814500_1.fastq.gz | Fastqsanger.gz | |||
| SRR20814500_2.fastq.gz | Fastqsanger.gz | |||
| SRR20814501_1.fastq.gz | Fastqsanger.gz | |||
| SRR20814501_2.fastq.gz | Fastqsanger.gz | |||
| SRR20814502_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 144 |
Similar Datasets
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Miscanthus x giganteus tissues (including leaves, flowers, and rhizomes). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves, flowers and rhizomes of Miscanthus x giganteus. Each tissue represented a mixture of developmental stages, with a bias towards those from early, actively differentiating cells. For rhizomes, the apical tip portion was collected. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Steven Moose for providing the plant material and Kan Nobuta for assistance with the computational methods.
2010-01-27 | E-GEOD-20056 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Miscanthus x giganteus tissues (including leaves, flowers, and rhizomes). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.
2010-01-27 | GSE20056 | GEO
Project description:In this study, we used transcriptomic and hormonomic approaches to examine drought-induced changes in barley roots and leaves and its rhizosphere. By studying hormonal responses, alternative splicing events in barley, and changes in the rhizosphere microbiome, we aimed to provide a comprehensive view of barley drought-adaptive mechanisms and potential plant-microbe interactions under drought stress. This approach improved our understanding of barley adaptive strategies and highlighted the importance of considering plant-microbe interactions in the context of climate change.
2024-10-31 | E-MTAB-14320 | biostudies-arrayexpress
Project description:Positive and negative ecological interactions shape the dynamics and composition of natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein-based, are not well understood and only a small percentage of such interactions has been studied. We hypothesize that secreted proteins are a powerful and highly specific toolset to shape and defend a favorable plant niche. Here, we have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to inhibit and promote the growth of bacteria through secretion of proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the secreted proteome of Albugo candida combined with machine-learning predictors enabled the selection of candidates for heterologous expression and study of their inhibitory activity in vitro. We found that three of the candidate proteins showed a selective antimicrobial activity on several gram-positive bacterial strains isolated from Arabidopsis thaliana. We could ascribe the antibacterial activity of the candidates to their intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins that have an antimicrobial activity under apoplastic conditions and therefore are potential biocontrol tools for a targeted manipulation of the microbiome.
2023-05-31 | PXD031981 | Pride
Project description:To explore mechanisms involved in the plant-microbe interactions, we proceeded with genome-wide transcriptome analysis of Arabidopsis roots incubated with E. coli Bl21 for 24 hours. Control plants did not receive E. coli.
2010-12-01 | GSE22277 | GEO
Project description:Miscanthus x giganteus Genome sequencing
| PRJNA337546 | ENA
Project description:Miscanthus x giganteus Genome sequencing
| PRJNA337545 | ENA