|
| Status |
Public on May 01, 2012 |
| Title |
Leaf of AT5 at selfed generation 5, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Leaf of AT5 at selfed generation 5
|
| Organism |
Triticum aestivum |
| Characteristics |
genotype/variation: synthetic allopolyploid lines
tissue: The 2nd leaf of 3-leaf-stage seedlings
|
| Treatment protocol |
The 2nd leaf of 3-leaf-stage seedlings was the source tissue for all RNA isolations.Pooled seedlings (10 plants for each replication) were used to represent each sample, with two biological replications.
|
| Growth protocol |
All plants, including the two synthetic lines and their respective parental lines, were grown in controlled growth chambers at 22/20°C day/night of 12 h day length.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogene) and purified through RNeasy Mini Spin Columns (Qiagen). The integrity of RNA was determined with an Agilent Bioanalyser 2100 Eukaryote Total RNA Nano Series II system. The 2nd leaf of 3-leaf-stage seedlings was the source tissue for all RNA isolations.
|
| Label |
biotin
|
| Label protocol |
According to the standard Affymetrix protocol(Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
According to the standard Affymetrix protocol(Expression Analysis Technical Manual, Affymetrix).
|
| Scan protocol |
According to the standard Affymetrix protocol(Expression Analysis Technical Manual, Affymetrix).
|
| Description |
Gene expression data from leaf
|
| Data processing |
The raw CEL data were normalized with the Robust Multichip Average (RMA)method using the R software 'limma' package. To identify differentially expressed genes, we used an empirical Bayesian based method to construct statistics and compute the relative p-values.Genes that were differentially expressed among genotypes were identified by a cut-off P value<0.05. The present (P) or absent (A) calls of each probeset was carried out by the MAS5 method using GCOS (Affymetrix Technologies) with default parameters. The differently expressed genes which did not show both present calls (P) in the two biological replications in at least one of the genotypes of each comparison were excluded from further analysis.
|
| |
|
| Submission date |
Jun 10, 2011 |
| Last update date |
May 01, 2012 |
| Contact name |
bao qi |
| E-mail(s) |
[email protected]
|
| Organization name |
chinese academy of science
|
| Street address |
5268 Renmin Street
|
| City |
changchun |
| ZIP/Postal code |
130024 |
| Country |
China |
| |
|
| Platform ID |
GPL3802 |
| Series (1) |
| GSE29882 |
Global transgenerational gene expression dynamics in two nascent allohexaploid wheat lines analogous in genome constitution to common wheat (Triticum aestivum) |
|
