|
| Status |
Public on Mar 12, 2012 |
| Title |
rice_control |
| Sample type |
SRA |
| |
|
| Source name |
inflorescences
|
| Organism |
Oryza sativa |
| Characteristics |
subspecies: Japonica
tissue: inflorescences
treatment: control
|
| Treatment protocol |
Four groups of plants are treated as follows: control (untreated), drought (drought for 3 days), cold (5 ˚C for 24 hours), and salt (400mM NaCl for 24 hours)
|
| Growth protocol |
Three-month-old plants grown at 28°C with 13h light
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from inflorescences and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 20 to 30 nt were excised and ligated to a preadenylated 3' adaptor and a 5’- adaptor using T4 RNA ligase. Ligation products were purified in polyacrylamide gels, followed by RT-PCR. The small RNA libraries were sequenced by the UCR core facility.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor, contain N, or have length less than 17nt were removed. The first column in a processed file contains clean reads, and the second column contains the number of copies of the reads in the library.
|
| |
|
| Submission date |
Dec 29, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Renyi Liu |
| E-mail(s) |
[email protected]
|
| Phone |
02157078228
|
| Organization name |
Shanghai Center for Plant Stress Biology
|
| Department |
Bioinformatics
|
| Street address |
3888 Chenhua Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL9147 |
| Series (1) |
| GSE26357 |
Genome-wide profiling of small RNAs in rice under abiotic stresses |
|
| Relations |
| SRA |
SRX037068 |
| BioSample |
SAMN00189360 |
