|
| Status |
Public on Apr 03, 2014 |
| Title |
F012 vs S028.F012_repl1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
whole 7 day old seedling
|
| Organism |
Zea mays |
| Characteristics |
genotype: F012
cultivar: Flint
|
| Growth protocol |
Inbred maize plants were grown in climate chamber under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 % air humidity) 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 either Cy5 or Cy3 following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA).
|
| |
|
| Channel 2 |
| Source name |
whole 7 day old seedling
|
| Organism |
Zea mays |
| Characteristics |
genotype: S028.F012
cultivar: interpool-hybrid
|
| Growth protocol |
Inbred maize plants were grown in climate chamber under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 % air humidity) 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 either Cy5 or 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 |
F012 vs S028.F012
|
| Data processing |
Data normalization was performed using the LIMMA package (version 2.9) from Bioconductor (Gentleman et al., Genome Biology 2004, 5:R80). For assessing differential expression, the normexp background correction method with the parameter offset=50 was applied to each array and resulted in strictly positive adjusted intensities. The adjusted signal intensities were normalized using a two-step normalization: weighted print-tip group loess normalization of log-ratios (within-array normalization) followed by quantile normalization of average log-intensities of two channels (between-array normalization). Between-array normalization for the two inbreds-hybrid comparisons P033.F047 and F047.P048 was seperately performed from the residual comparisons. A series of positive control probes were given double weight to assist the normalization process.
Provided supplementary file contains mean normalized log2 expression value of each gene-related oligo of each genotype from an inbreds-hybrid comparison. The values consists of normalized replicate values from two arrays of the total three arrays of each inbreds-hybrid comparison. For example "1_F012 (F012.P024)" describes the normalized expression of the genotype F012 derived from the comparison of the hybrid F012.P024 and its inbred parents. These data represent the absolute values used in the associated manuscript.
|
| |
|
| Submission date |
Nov 15, 2013 |
| Last update date |
Apr 03, 2014 |
| Contact name |
Stefan Scholten |
| E-mail(s) |
stefan.scholten@uni-hamburg.de
|
| Phone |
0049 40 42816329
|
| Organization name |
University of Hamburg
|
| Department |
Biocenter Klein Flottbek
|
| Lab |
Developmental Biology and Biotechnology
|
| Street address |
Ohnhorststrasse 18
|
| City |
Hamburg |
| State/province |
Hamburg |
| ZIP/Postal code |
22609 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17936 |
| Series (1) |
| GSE52411 |
Gene expression analysis of nine European maize (Zea mays L.) inbred lines and nine corresponding hybrids |
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