Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-38612
PROVIDER: PRJNA168212 | ENA |
REPOSITORIES: ENA
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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: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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