|
| Status |
Public on Jun 04, 2012 |
| Title |
Cotton control 20 dpa sample, biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Cotton control plant
|
| Organism |
Gossypium hirsutum |
| Characteristics |
cultivar: Bikaneri Nerma
developmental stage: 20 dpa sample
treatment: control
|
| Treatment protocol |
Cotton bolls at 20 dpa were collected from drought induced and control plants and immediately frozen in liquid nitrogen.
|
| Growth protocol |
G. hirsutum cv. Bikaneri Nerma was used in the present study. A rain out shelter (ROS) was specifically created at the University of Agricultural Sciences (UAS), Dharwad, Karnataka, India for creating and maintaining desired drought stress at various stages during the fibre development. Plants were grown in twelve adjacent plots (six for control and six for drought induction) in the open filed. The ROS was used to cover six plots only when there was a rain to maintain the drought stress conditions. Watering was withheld during peak flowering stage for the induction of drought stress. Soil moisture content (SMC) was recorded every alternate day after stopping irrigation. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. This condition was observed 18-19 days after stopping the irrigation. About 20% of the soil moisture content was maintained throughout the sample collection period by spraying water if and when required. Samples at 20 dpa were collected from drought induced and control plots.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from fibre bearing ovules of 20 dpa collected from drought induced and control plants.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5.0 µg total RNA Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.
|
| Scan protocol |
The cotton GeneChip Genome arrays were scanned on a GeneChip scanner 3000.
|
| Description |
Gene expression data of 20 dpa sample of control cotton plant
|
| Data processing |
After scannig CEL files were analyzed using GeneSpring GX 11.0 software. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed.
|
| |
|
| Submission date |
May 26, 2011 |
| Last update date |
Jun 04, 2012 |
| Contact name |
Padmalatha K.V. |
| E-mail(s) |
[email protected]
|
| Phone |
09953789208
|
| Organization name |
NRCPB
|
| Department |
Plant Biotechnology
|
| Lab |
Bt.lab
|
| Street address |
Pusa campus
|
| City |
New delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110012 |
| Country |
India |
| |
|
| Platform ID |
GPL8672 |
| Series (2) |
| GSE29567 |
Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages. |
| GSE29810 |
Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue and during fibre development stages. |
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