|
| Status |
Public on Dec 22, 2008 |
| Title |
kernel_susceptible1_water stress_vs_well watered_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL 66 grown in well watered field condition and labeled with cyanine 5
|
| Organism |
Zea mays |
| Characteristics |
RIL from B73xH99
phenotypically recorded as susceptible (RIL66)
organ: 10days after pollination kernels
well watered: 30% (expressed on a dry weight basis) soil moisture was maintained for the treatment
|
| Treatment protocol |
Two levels of drought treatment were applied, well watered and water stress, with two randomized blocks for each level. For each block, two rows of fifteen plants per genotype were grown at a plant density of four plants/square meter. All trials were well irrigated from sowing to the start of the treatment. Thereafter, the well-watered trials received additional full irrigations maintaining soil moisture at about 30% expressed on a dry weight basis, while stressed plants received just enough water for surviving (soil moisture about 16%). The stress was applied strarting three weeks before flowering time.
|
| Growth protocol |
All plants were grown in open field in Foggia (Southern Italy) where in late spring and summer the temperature is high and the rainfall is usually very limited or absent. Therefore the water supply was tightly controlled by differential irrigation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, from a pool of 6-9 kernels (2-3 seeds from 3 different ears) at 10 DAP, using LiCl based method. RNA quality was evaluated on agarose gels and assorbance 260/280 ratios between 1.8 and 2.2 were typically obtained. Poly(A+) RNA was purfied using the Amersham mRNA Purification Kit (GE Healthcare, NJ, USA).
|
| Label |
Cy5
|
| Label protocol |
1µg of purified poly(A+) RNA was labeled according to the protocol of the Amersham CyScribe Post-Labeling Kit (GE Healthcare, NJ, USA)
|
| |
|
| Channel 2 |
| Source name |
poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL 66 grown in well water stress field condition and labeled with cyanine 3
|
| Organism |
Zea mays |
| Characteristics |
RIL from B73xH99
phenotypically recorded as susceptible (RIL66)
organ: 10days after pollination kernels
water stress: 16% (expressed on a dry weight basis) soil moisture was maintained for the treatment
|
| Treatment protocol |
Two levels of drought treatment were applied, well watered and water stress, with two randomized blocks for each level. For each block, two rows of fifteen plants per genotype were grown at a plant density of four plants/square meter. All trials were well irrigated from sowing to the start of the treatment. Thereafter, the well-watered trials received additional full irrigations maintaining soil moisture at about 30% expressed on a dry weight basis, while stressed plants received just enough water for surviving (soil moisture about 16%). The stress was applied strarting three weeks before flowering time.
|
| Growth protocol |
All plants were grown in open field in Foggia (Southern Italy) where in late spring and summer the temperature is high and the rainfall is usually very limited or absent. Therefore the water supply was tightly controlled by differential irrigation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, from a pool of 6-9 kernels (2-3 seeds from 3 different ears) at 10 DAP, using LiCl based method. RNA quality was evaluated on agarose gels and assorbance 260/280 ratios between 1.8 and 2.2 were typically obtained. Poly(A+) RNA was purfied using the Amersham mRNA Purification Kit (GE Healthcare, NJ, USA).
|
| Label |
Cy3
|
| Label protocol |
1µg of purified poly(A+) RNA was labeled according to the protocol of the Amersham CyScribe Post-Labeling Kit (GE Healthcare, NJ, USA)
|
| |
|
| |
| Hybridization protocol |
The slides were hybridized using the procol described in the MWG Array manual (http://ecom2.mwgdna.com/services/array/download)
|
| Scan protocol |
Images were acquired at 5µm resolution by ScanArray v3.1 software on SA4000 Scanner (Packard Bioscience, Wellesley, MA) and quantified using Quantarray v3.0 software (Packard Bioscience, Wellesley, MA)
|
| Description |
ch2/ch1 (water stress/well watered)
|
| Data processing |
Local background subtraction, per chip LOWESS and 50th percentile within array normalization function were performed by Genespring (Agilent Techonologies, Palo Alto,CA)
|
| |
|
| Submission date |
May 27, 2008 |
| Last update date |
Dec 22, 2008 |
| Contact name |
Rosanna Marino |
| E-mail(s) |
rosanna.marino@unimi.it
|
| Phone |
00390250315042
|
| Fax |
00390250315044
|
| URL |
http://users.unimi.it/camelot/
|
| Organization name |
Universita' degli studi di Milano
|
| Department |
Department of biomolecular sciences and biothecnology
|
| Lab |
Plant molecular genetics
|
| Street address |
Via celoria 26
|
| City |
Milano |
| State/province |
Milano |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6906 |
| Series (1) |
| GSE11568 |
Transcriptional profiling of Zea mays 10 DAP(days after pollination) kernels : water stress vs well-watered control |
|
