Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-38612
PROVIDER: PRJNA168212 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Small RNA identification in Arabidopsis thaliana using modified MPSS
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Project description:Small RNA identification in Arabidopsis thaliana using 454 data
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Project description:In this project, we profiled the dynamics of proteome during Arabidopsis early embryogenesis using nanoproteomics. In addition, we identified some proteins which may be important during this process. Combining with RNA-seq, we unveiled the relationship between RNA and proteins during Arabidopsis early embryogenesis.
2022-09-07 | PXD031922 | Pride
Project description:To explore the overall long noncoding RNA (lncRNA) involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (4 rosette leaves>1mm, 14 rosette leaves>1mm, rosette growth complete, first flower buds visible, flourishing florescence, first silique shattered, senescence) using strand-specific RNA sequencing (ssRNA-seq) menthod. We obtained 28.8 Gb raw data and identified 156 novel lncRNAs (unreported in all public plant lncRNA databases) . We also categorized the novel lncRNAs as intergenic, intronic, antisense, overlapped with perhaps pseudogenes and mRNA based on their location on the Arabidopsis genome. Furthermore, lncRNAs targeted protein-coding genes were predicted and functional annotated. In addition, we constructed a network of interactions between ncRNAs (miRNAs, lncRNA) and mRNAs. Our results suggest that the identified novel lncRNAs are important in modulating development process of Arabidopsis, and provide a rich resource for further research on the function of these novel lncRNAs.
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Project description:Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)
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Project description:It is increasingly evident that various RNA molecules can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA-chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than ten thousand RNA-chromatin interactions mediated by protein-coding RNAs, long non-coding RNAs (ncRNAs) and small ncRNAs in Arabidopsis. These RNAs preferentially target genic regions, especially exonic regions. Protein-coding RNAs primarily engage in local and cis-chromosomal interactions, whereas long ncRNAs (lncRNAs) and small ncRNAs preferentially engage in trans-chromosomal interactions. RNA-chromatin interactions tend to positively correlate with DNA-DNA interactions, suggesting a role of DNA-DNA interactions in confining RNA-chromatin interactions and/or a role of RNA-chromatin interactions in shaping genome organization at a global level. We further show that some RNA-chromatin interactions undergo alterations in response to biotic and abiotic stresses. Our study provides a global view of RNA-chromatin interactions in Arabidopsis and a rich resource for future investigation of the regulatory roles of RNAs in gene expression and genome organization.
2021-08-27 | GSE163845 | GEO
Project description:Transcriptome profiling of Arabidopsis using strand-specific RNA-seq
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Project description:Identification of CLF-regulated transcripts using strand-specific RNA-sequencing in Arabidopsis
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Project description:We profiled Arabidopsis transcriptom using RNA-seq. Each RNA library yielded 223-250 million 101-bp single-end reads (235M on average). Using Tophat and Cufflinks, 30,199~30,650 assembled transcripts were identified in each of 4 samples. Of them, 1340 ones were derived from intergenic regions including 278 long intergenic ncRNAs (LincRNAs). Comparing with the 6,480 lincRNAs we identified by analysis of 200 tiling array data sets, 2,708 lincRNAs were also detected by RNA-seq.
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Project description:Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50~300nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half (58%) are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5’-UTR derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited significantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epigenetic mechanisms as those of protein-coding genes, and some showed developmentally-regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally-regulated and functional components discovered in the transcriptome.
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