|
| Status |
Public on Dec 26, 2012 |
| Title |
Oxidative stress during cold stress 3 |
| Sample type |
RNA |
| |
|
| Source name |
Oxidative stress during cold stress 3
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
cultivar: Pusa Basmati (PB1)
age: 10-days old
tissue: whole seedling
oxidative stress: concurrent oxidative stress
temperature stress: cold stress
|
| Treatment protocol |
For oxidative Stress prior to High Temperature Stress (PO_HS) or Low Temperature Stress (PO_CS) uniformly grown seedlings (10 day old) were transferred to beakers, which contain 10mM H2O2 at 28+2oC for oxidative stress (OS) for 4 h and followed by heat stress (HS) 42+1oC for 30 minutes/ cold stress (HS) 5+1oC for 5 h in the growth chamber with lights on. Similarly for oxidative Stress during High Temperature Stress (DO_HS)/ during Low temperature stress (DO_CS) uniformly grown seedlings (10 day old) were transferred to beakers, which contain 10mM H2O2 maintained at 42+1oC for heat stress (HS) for 30 minutes/5+1oC for cold stress (CS) in the BOD with lights on. All Samples were harvested, frozen in liquid nitrogen and kept at -80°C immediately after stress treatment.
|
| Growth protocol |
Seedlings were grown at 28+2oC and 14 h light/ 10 h dark cycle maintained in growth room (light intensity ~250µmol.m-2.s-2, humidity 40-50%) for 10 d.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ~100 mg tissue using Tri- Reagent (Sigma, USA) as per the manufacturer’s instructions, and further purified using RNAesy Mini Elute Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (200ng) was labeled with Cy3 using Agilent Low RNA Input fluorescent Linear Amplification Kit (Agilent Technologies). Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
Hybridization and wash processes were performed according to the manufacturer’s instructions.
|
| Scan protocol |
Hybridized microarrays were scanned using agilent microarray scanner (g2505b, agilent technologies, usa) at 5µ resolution.
|
| Description |
Oryza sativa ssp. indica L; cultivar Pusa Basmati (PB1)
DO_CS3
Oxidative stress during cold stress replicate 3
Agilent Feature Extraction file
US83000164_251524112328_S01_GE1_105_Dec08_1_1.txt
|
| Data processing |
Feature extraction software (version 10.5.1.1 Agilent Technologies, USA) was employed for the image analysis and data extraction process. The normalization was done using GeneSpring GX 10.2 (Agilent Technologies, USA) using the recommended Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile Per Gene: Normalize to Specific Samples (Treated Vs Control). Data analysis was done using GeneSpring GX version 7.3.1 (Agilent Technologies, USA) and Microsoft Excel. In total three biological replicates were processed in a similar manner for the microarray analysis. Genes showing differential expression (up or down) by 2 fold or more (log2 values) with a p- value less than or equal to 0.05 were considered statistically significant.
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| |
|
| Submission date |
Oct 12, 2011 |
| Last update date |
Dec 26, 2012 |
| Contact name |
Anil Grover |
| E-mail(s) |
anil.anilgrover@gmail.com
|
| Phone |
91-11-24117693
|
| Fax |
91-11-24115270
|
| URL |
http://www.south.du.ac.in/dpmb/index.php?page=anil-grover
|
| Organization name |
University of Delhi South Campus
|
| Department |
Plant Molecular Biology
|
| Lab |
Stress Biology Lab
|
| Street address |
Benito Juarez Road
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110021 |
| Country |
India |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE32704 |
Transcriptional changes in response to oxidative stress in combination with temperature extremes in rice |
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