|
| Status |
Public on Nov 01, 2012 |
| Title |
A188_highN_d20_3 |
| Sample type |
RNA |
| |
|
| Source name |
lamina fifth leaf
|
| Organism |
Zea mays |
| Characteristics |
inbred line: A188
treatment: 15mM nitrate supply
plant age: 20 days
|
| Treatment protocol |
Fertilization started at day seven after germination with a modified Hoagland solution (5mM CaCl2, 2mM MgSO4, 2mg/L Fe, 0.5mM KH2PO4, 50µM H3BO4, 10µM MnCl2, 1µM ZnSO4, 0.3µM CuSO4, 0.5µM Na2MoO4). Depending on N treatment scheme, the nutrient solution contained 15mM for high N treatment or 0.15mM KNO3 for low N treatment. The differences in potassium supply were balanced with KCl. Plants received 100ml of nutrient solution every third day, between the fertilisation supply, plants were watered with distilled water depending on water status in the pot. The last watering with nutrient solution always happened two days before the harvest.
|
| Growth protocol |
Zea mays seeds of genotypes A188 and B73 were germinated on wet filter paper and transferred into pots of 1.5L volume containing nutrient poor peat soil (Basissubstrat 2, Klasmann& Deilmann, Germany). Plants were either fertilized with high N (15mM nitrate) or low N (0.15mM nitrate) supplied Hoagland solution. Growth conditions in the plant climate chamber (PlantMaster PGR 3045, CLF Plant Climatics GmbH, Germany) were set at diurnal rhythm of 14h light (ca. 200 µmol m-2 s-1 at level of the soil surface and ca. 650 µmol m-2 s-1 just under the light source which was adjusted according to plant height to give maximal possible irradiance) at 28°C and 80% humidity, and 10h night at 20°C and 50% humidity. Harvest of plant material always started two hours after start of the light period and was always completed before midday.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from four biological replicates per genotype, growth stage and treatment after the method described by Logemann et al. (1987) using 100mg of frozen leaf material. The isolated RNA was purified with the RNeasy purification kit according to the manufacturer’s instructions (Qiagen, Germany). The quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit.
|
| Label |
Cy3
|
| Label protocol |
The cDNA and following antisense cRNA synthesis was performed according to the one-color microarray-based gene expression analysis protocol (Agilent).
|
| |
|
| Hybridization protocol |
An aliquot of 1.65 mg of RNA was loaded on one-color microarrays with custom-designed oligonucleotide probes (Agilent 025271).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent G2565B Microarray Scanner.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent) using default parameters (protocol GE-v5_95_Feb07). The processed signals were log2 transformed and normalised to the 75th percentile within each array followed by median base line correction using the Agilent GeneSpring GX 11.0 software.
|
| |
|
| Submission date |
Sep 07, 2012 |
| Last update date |
Nov 01, 2012 |
| Contact name |
Urte Schluter |
| E-mail(s) |
schluter@biologie.uni-erlangen.de
|
| Phone |
+49 9131 85 28860
|
| Fax |
+49 9131 85 28854
|
| Organization name |
FA University Erlangen
|
| Department |
Biology
|
| Lab |
Biochemistry
|
| Street address |
Staudtstr. 5
|
| City |
Erlangen |
| ZIP/Postal code |
91058 |
| Country |
Germany |
| |
|
| Platform ID |
GPL14913 |
| Series (1) |
| GSE40678 |
Maize source leaf metabolism under high (15mM) or low (0.15mM) nitrogen supply |
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