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| Status |
Public on Jun 06, 2012 |
| Title |
non-coding RNA sequencing of upland cotton fiber and ovule |
| Organism |
Gossypium hirsutum |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.Cotton plants (Gossypium hirsutum cv. Xuzhou 142) were grown in a soil mixture in fully automated walk-in growth rooms with 300 µmol m–2 s–1 average light intensity, 60% relative humidity and temperatures set to 30C during the light period and 28C during the dark (12-h light/dark cycle). These conditions were consistent throughout the year. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer IIx according to the manufacturer's instructions. The 38nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and clipping adapter sequences.
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| Overall design |
Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.
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| Contributor(s) |
Li Q, Jin X, Xiao G, Zhu Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu-Xian Zhu |
| E-mail(s) |
zhuyx@water.pku.edu.cn
|
| Phone |
86-10-62751193
|
| Fax |
86-10-62754427
|
| Organization name |
College of life sciences, Peking University
|
| Lab |
National Lab of Protein Engineering & Plant Genetic Engineering
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| Street address |
5# Summer Palace Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (1) |
| GPL14001 |
Illumina Genome Analyzer IIx (Gossypium hirsutum) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA158285 |
| SRA |
SRP012138 |
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