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| Status |
Public on Jul 27, 2012 |
| Title |
Global identification and characterization of intermediate-size non-coding RNAs in Oryza sativa |
| Organism |
Oryza sativa |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5’ and 3’ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.
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| Overall design |
Examination of non-coding RNA in 2 stages in Oryza sativa, using 454 deep sequecing
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| Contributor(s) |
Liu T, Chen W |
| Citation(s) |
22986792 |
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| Submission date |
Jul 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Chen |
| E-mail(s) |
cnchw@163.com
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| Organization name |
Peking University
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| Street address |
No.5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (1) |
| GPL15856 |
454 GS FLX Titanium (Oryza sativa) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA171494 |
| SRA |
SRP014594 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE39695_RAW.tar |
30.0 Kb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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