|
| Status |
Public on Aug 21, 2010 |
| Title |
F039 vs S046 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
F039
|
| Organism |
Zea mays |
| Characteristics |
inbred line: F039
cultivar: flint
tissue: seedling
age: 7 day
sample type: pool of 5 biological replicates
|
| Growth protocol |
Regulated growth conditions (25℃ 16h-day, 21℃ 8h-night, 70% air humidity) in a climate chamber (Percival Scientific Inc., Perry, USA) for seven days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with an extraction buffer (200 mM NaCl, 50mM Tris pH 9, 5 mM EDTA pH 8, 1% SDS), phenol/chloroform and selective LiCl (4M) precipitation.
|
| Label |
Cy5
|
| Label protocol |
Aminoallyl-RNA was labeled with Cy5 following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA).
|
| |
|
| Channel 2 |
| Source name |
S046
|
| Organism |
Zea mays |
| Characteristics |
inbred line: S046
cultivar: dent
tissue: seedling
age: 7 day
sample type: pool of 5 biological replicates
|
| Growth protocol |
Regulated growth conditions (25℃ 16h-day, 21℃ 8h-night, 70% air humidity) in a climate chamber (Percival Scientific Inc., Perry, USA) for seven days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with an extraction buffer (200 mM NaCl, 50mM Tris pH 9, 5 mM EDTA pH 8, 1% SDS), phenol/chloroform and selective LiCl (4M) precipitation.
|
| Label |
Cy3
|
| Label protocol |
Aminoallyl-RNA was labeled with Cy3 following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA).
|
| |
|
| |
| Hybridization protocol |
The hybridization and post-hybridization followed the protocol of the Maize Oligo Array Project (http://www.maizearray.org/).
|
| Scan protocol |
The slides were scanned using an AppliedPrecision ArrayWorx Scanner (Applied Precision Inc., USA).
|
| Description |
Gene expression data from European maize inbred lines (14 dent, 7 flint)
|
| Data processing |
Raw data from microarray hybridization, exported from GenePix suites 6.0 (Axon, USA), was imported into LIMMA. The background was corrected by normexp method with offset 50. Background-corrected signal intensities were normalized using a two-step normalization: print-tip group loss (within-array normalization) and then between-array scale normalization.
|
| |
|
| Submission date |
Aug 21, 2009 |
| Last update date |
Aug 25, 2009 |
| Contact name |
Stefan Scholten |
| E-mail(s) |
stefanscholten@botanik.uni-hamburg.de
|
| Phone |
0049 40 42816329
|
| Fax |
0049 40 42816229
|
| Organization name |
University of Hamburg
|
| Department |
Biocenter Klein Flottbek
|
| Lab |
Developmental Biology and Biotechnology
|
| Street address |
Ohnhorststrasse 18
|
| City |
Hamburg |
| ZIP/Postal code |
22609 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6438 |
| Series (1) |
| GSE17754 |
Genome-wide analysis of gene expression profiles of 21 European maize (Zea mays L.) inbred lines. |
|
