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| Status |
Public on Mar 07, 2021 |
| Title |
small RNA sequencing from leaf of Arabidopsis to identify tsRNA |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
tsRNA is newly found small non-coding RNA with important biological function. However, the knowlede of diversity, biogeneis and function of tsRNA in plant is still lacking. Here, we selected 10-60 nt small RNA for high-throughput sequencing and uncovered the diversity,biogenesis and potentical function of tsRNA in Arabidopsis.
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| Overall design |
Col-0, dcl1-7 and PTH-AGO1 transgenic plants were grown under long-day (16h light) condition at 23°C. Leaves of four week old plants were harvested 3 h after wounding, or as control leaves without wounding. One gram of wild type (WT-IP) or PTH-AGO1 (AGO1-IP) transgenic plant leaves was ground in liquid nitrogen and dissolved in 5 mL lysis buffer (50mM Tris-HCl at pH 7.5, 150 mM NaCl, 5 mM MgCl2, 0.5% NP-40, 5 mM DTT and protease inhibitor). After centrifugation, supernatants were incubated with IgG Sepharose 6 Fast Flow agarose beads (GE Healthcare) and rotated for 1 h at 4 °C. The beads were washed five times with lysis buffer. RNA in the immunoprecipitates was recovered with TRIzol reagent (Ambion). Total RNA or IP RNA was fractionated by electrophoresis. RNA from 10 to 60 nt was sliced and recovered. The purified small RNA was subjected to adapter ligation, reverse transcription, PCR amplification with NEXTflex Small RNA Sequencing Kit (Bioo Scientific), and the resulting libraries sent for deep sequencing by Illumina HiSeq2000. For total RNA from wild type and dcl1-7 plants, small RNA libraries were made independently from two biological replicates. WT-IP, AGO1-IP, and its input libraries were made independently from three biological replicates.
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| Contributor(s) |
Zhu L, Liug X, Dong Z |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 07, 2017 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Zhicheng Dong |
| E-mail(s) |
zc_dong@gzhu.edu.cn
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| Organization name |
Guangzhou University
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| Department |
School of Life Sciences
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| Street address |
230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510006 |
| Country |
China |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA378353 |
| SRA |
SRP101483 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95768_RAW.tar |
192.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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