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| Status |
Public on Jul 13, 2017 |
| Title |
Deep sequencing of uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Our previous experiment on biogenesis mechanisim of stress-inducible antisense RNAs showed that accumulation of antisense RNA in a drought-inducible gene, RD29A locus was decreased in rdr1/2/6 triple mutant. The RD29A antisense RNA did not have CAP structure and poly(A) tail. We applied deep sequencing of uncapped RNA using SOLiD to identify RDR1/2/6-mediated antisense RNAs in genome-wide. We identified 1) 975 RDR1/2/6-mediated antisense RNA loci on which no. of sequence tags is decreased in rdr1/2/6 and makes peak and 2) 1,613 RDR1/2/6-mediated antisense RNA loci on which no. of the tags is decreased in rdr1/2/6 and enriched on antisense strand of exons. They were grouped into 1,959 non-redundant loci.
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| Overall design |
Untreated and 2hr drought stress-treated 2 weeks-old rdr1/2/6 and wild-type Arabidopsis thaliana plants were used. To determine 5’-end of uncapped RNA with and without poly (A), we developed Deep Sequencing of Uncapped RNAs (DSUR) with reference to PARE analysis (German et al. 2009, Nature Protocol 4:356-362) and applied DSUR using SOLiD to identify genome-wide RDR1/2/6-mediated antisense RNA loci in Arabidopsis.
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| Contributor(s) |
Matsui A, Iida K, Tanaka M, Ishida J, Morosawa T, Yamaguchi K, Shigenobu S, Kobayashi N, Toyoda T, Seki M |
| Citation missing |
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| |
| Submission date |
Jun 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Motoaki Seki |
| E-mail(s) |
motoaki.seki@riken.jp
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| Organization name |
RIKEN CSRS
|
| Street address |
1-7-22, Suehiro-cho, Tsurumi
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| City |
Yokohama |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platforms (1) |
| GPL14599 |
AB SOLiD 4 System (Arabidopsis thaliana) |
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| Samples (4)
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| GSM954261 |
rdr1/2/6 under drought stress (dsur) |
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| This SubSeries is part of SuperSeries: |
| GSE39037 |
Deep sequencing of small and uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants |
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| Relations |
| BioProject |
PRJNA169644 |
| SRA |
SRP013992 |
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