|
| Status |
Public on Dec 21, 2011 |
| Title |
Slice6_reps1-4 |
| Sample type |
RNA |
| |
|
| Source name |
third leaf, 18cm length
|
| Organism |
Zea mays |
| Characteristics |
tissue: third leaf
slice (slice1=oldest, slice10=youngest): Slice6
|
| Treatment protocol |
No treatment was applied
|
| Growth protocol |
Z. mays plants of the ecotype B73 were grown in the greenhouse for 14 to 15 days in clay pots in Floraton soil. Natural light, a shading system and artificial light were used to extend the daylight period to 16 hours at a photon flux density of approximately 500 μmol m-2 s-1. The humidity in the greenhouse was between 75 and 90%. The green house’s ventilation system kept the temperature at 24°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The 3rd leaf was harvested at 18cm length measured from tip to emergence from the stem. Leaves were harvested by placing them atop a custom made leaf guillotine where they were snap frozen. By closing the lid, the leaf is cut into ten pieces of 2cm width, the last of which had not yet emerged. Twenty plants were pooled for each biological replicate. The mRNA was isolated after the method of Logemann et al. (1987) and from the same plant material the enzyme activities and metabolites were measured of. The isolated RNA was purified with the RNeasy Purification Kit according to the producer’s instruction (Qiagen). The quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit. The cDNA and following antisense cRNA synthesis was performed according the one-color microarray-based gene expression analysis protocol (Agilent ). An aliquot of 1.65 µg of this RNA was loaded on one-color microarrays with custom designed oligonucleotide probes (Agilent 025271).
|
| Label |
Cy3
|
| Label protocol |
The cDNA and following antisense cRNA synthesis was performed according the one-color microarray-based gene expression analysis protocol (Agilent).
|
| |
|
| Hybridization protocol |
An aliquot of 1.65 µg of this RNA was loaded on one-color microarrays with custom designed oligonucleotide probes (Agilent 025271)
|
| Scan protocol |
Arrays were scanned according to manufacturer's standard protocols.
|
| Description |
Gene expression based on physical location in a leaf
|
| Data processing |
Transcripts were normalized to the 75th percentile within each array using the Agilent Gene spring program. For K-means clustering and hierachical clustering, four replicates were averaged.
|
| |
|
| Submission date |
Nov 22, 2011 |
| Last update date |
Dec 21, 2011 |
| Contact name |
Andrea Braeutigam |
| E-mail(s) |
andrea.braeutigam@uni-duesseldorf.de
|
| Organization name |
Heinrich Heine University Duesseldorf
|
| Department |
Botany
|
| Lab |
Plant Biochemistry
|
| Street address |
Universitaetsstrasse 1
|
| City |
Duesseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL14913 |
| Series (1) |
| GSE33861 |
Gradient of the third maize leaf of a 14 day old plant |
|
