|
| Status |
Public on Mar 12, 2010 |
| Title |
Rice_AGO4b |
| Sample type |
SRA |
| |
|
| Source name |
Wild type seedling
|
| Organism |
Oryza sativa |
| Characteristics |
protein complex: AGO4b
|
| Treatment protocol |
RNAs were extracted from total extract and immunopurified AGO4 complexes by Trizol reagents. Bigger RNAs were removed by PEG precipitation, and enriched small RNAs were seperated on 15% PAGE/7M Urea gel, and small RNA within the range of 18-28 nt were purified from the gel.
|
| Growth protocol |
Rice plants were gorwn in growth chambers with 12-h light/dark cycles, 28 oC during the day and 23 oC during the night.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs were ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified using a pair of Illumina cloning primers and then provided for Illumina sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
The adaptor sequences in Illumina 1G sequencing reads were removed by using ‘‘vectorstrip’’ in the EMBOSS package. The small RNA reads with length of 19–27 nt were mapped to the genome using Blast. small RNAs with match to transgenic inverted-repeat or without perfect match to the genome were removed.
|
| |
|
| Submission date |
Mar 11, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijun Qi |
| E-mail(s) |
qiyijun@nibs.ac.cn
|
| Phone |
86-10-80727837
|
| Fax |
86-10-80727873
|
| URL |
http://www.nibs.ac.cn/?act=view&id=726
|
| Organization name |
National Institute of Biological Sciences, Beijing
|
| Street address |
No.7 Science Park Road,Zhongguancun Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL9147 |
| Series (1) |
| GSE20748 |
DNA Methylation Mediated by a MicroRNA Pathway |
|
| Relations |
| SRA |
SRX017395 |
| BioSample |
SAMN00009678 |
