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| Status |
Public on Jul 22, 2017 |
| Title |
Genome-wide identification and characterization of novel lncRNAs in Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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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| Overall design |
RNA-sequencing of whole plants at 7 developmental stages (pooled sample).
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| Contributor(s) |
Jin B, Lu Z |
| Citation(s) |
28499866 |
| Submission date |
Apr 24, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Biao Jin |
| E-mail(s) |
bjin@yzu.edu.cn
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| Phone |
13056359569
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| Organization name |
Yangzhou University
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| Department |
College of Horticulture and Plant Protection
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| Lab |
Jin Lab
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| Street address |
Wenhui east road no. 48
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| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA384090 |
| SRA |
SRP105133 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98141_RAW.tar |
10.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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