|
| Status |
Public on Jun 30, 2020 |
| Title |
HD2967 Nitrogen control root, Rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
HD2967 wheat genotype 15-d old root tissue N control
|
| Organism |
Triticum aestivum |
| Characteristics |
genotype/variation: HD2967
group: N control
tissue: 15 day old wheat root tissue
|
| Treatment protocol |
All four genotypes were grown in two different conditions: MS modified (without N source) medium with standard nitrogen nutrition (control/+N) including 8mM Ca(NO3)2, and nitrogen starved condition (stressed/-N), with 0.08mM Ca(NO3)2 as source.
|
| Growth protocol |
Uniform size seeds of all four varieties were surface sterilized using 0.1% sodium hypochlorite for 5 min and then rinsed three times with sterile water. The sterilized seeds were germinated in water soaked filter paper placed in Petriplates at 25±1°C in the dark. When the primary roots were grown approximately 1cm in length, the germinating seeds were transferred in pots (5 seeds/pot) containing mixture of vermiculite and perlite in a ratio 2:1 and grown for 15 days in the culture room under a 16/8h light/ dark conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen, Valencia, USA) and treated with DNaseI (Qiagen) according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
250ng of total RNA were incubated with Oligo dT/T7 primers and reverse -transcribed into double stranded cDNA. The amplified RNA were purified and labeled by biotin with GeneChip® IVT labeling kit.
|
| |
|
| Hybridization protocol |
The biotinylated cDNAs were fragmented and hybridized to the Affymetrix GeneChip® Wheat Genome Array (Affymetrix, Inc., Carlsbad, CA) for 16 hours. The arrays were processed according to the manufacturer's specifications.
|
| Scan protocol |
GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Gene expression data from 15 day old root tissue of nitrogen control (8 mM) HD2967 wheat variety, replicate 2
|
| Data processing |
The data were analyzed using affymetrix GeneChip command console software (AGCC) and Robust MultiChip Average (RMA) used for normalization of data. Each array dataset was then imported into Agilent GeneSpring software 14.5 for analysis.
|
| |
|
| Submission date |
Jul 01, 2018 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Pranab kumar Mandal |
| E-mail(s) |
pranab.mandal@icar.gov.in
|
| Phone |
011-25841787
|
| Organization name |
Indian council of Agriculture Research
|
| Department |
National Research Centre on Plant Biotechnology
|
| Lab |
Dr. P.K. Mandal
|
| Street address |
LBS building, Pusa Campus
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110012 |
| Country |
India |
| |
|
| Platform ID |
GPL3802 |
| Series (1) |
| GSE116473 |
Expression data of four wheat genotypes viz. HD2967, K307, K9107 and Chotilarma (CL) in response to nitrogen chronic limitation |
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