|
| Status |
Public on Mar 01, 2012 |
| Title |
High salinity treated_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
High salinity treated
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nakdong
genotype/variation: wild type (nontransgenic)
tissue source: 14d-old seedlings
tissue: root
|
| Growth protocol |
Rice (Oryza sativa cv Nakdong) seeds were germinated in half-strength MS solid medium in a growth chamber in the dark at 28ºC for 4 d, transplanted into soil and then grown in a greenhouse (16-h-light/8-h-dark cycles) at 28-30ºC for two weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
S_2
This sample is total RNAs of high salinity treated rice
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Sep 05, 2011 |
| Last update date |
Mar 01, 2012 |
| Contact name |
Jin Seo Jeong |
| E-mail(s) |
jsjeong74@gmail.com
|
| Organization name |
Myongji University
|
| Street address |
San 38-2 Namdong, Cheoin-gu
|
| City |
Yongin |
| State/province |
Gyeonggido |
| ZIP/Postal code |
449-728 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL7344 |
| Series (1) |
| GSE31874 |
Expression analysis of abiotic stress-treated rice |
|
