|
| Status |
Public on Sep 16, 2009 |
| Title |
Lemma_Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Lemma
|
| Organism |
Hordeum vulgare |
| Characteristics |
tissue: Lemma
|
| Growth protocol |
Barley plants (Hordeum vulgare L.) cv. Morex were grown in a controlled environment chamber at 22°C/18°C day/night temperatures, 60% RH and a 16 h photoperiod. Plants were grown in 20 cm x 25 cm pots and fertilized using Osmocote® slow release fertilizer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the lemma, the palea and the awn was extracted with guanidinium thiocyanate (Chirgwin et al. 1979). Total RNA from the seed was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH), followed by precipitation of starch with 0.8 M sodium citrate and 1.2 M NaCl according to the manufacturer’s recommendation.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA was prepared from total RNA according to the the Affymetrix One-Cycle Target Labeling protocol.
|
| |
|
| Hybridization protocol |
The labeled cRNA was purified and fragmented. Then, hybridization controls were added to the resulting cRNA and hybridized to the Barley1 GeneChips for 16 h at 45°C. Arrays were washed using the GeneChip® Fluidics Station 450.
|
| Scan protocol |
GenChips were scanned using the GeneChip® 3000 Scanner.
|
| Description |
This is biological replication 2 for lemma collected at the grain-filling stage.
|
| Data processing |
Cell intensity (CEL) files were imported into Expression Console v 1.1 (Affymetrix) for background correction and normalization using the Microarray Analysis Suite v 5.0 (MAS5) algorithm. Background intensity was corrected as the difference between the perfect match (PM) and mismatch (MM) pair of each probe set. Summarised values were normalized using global scaling. The mean signal of each array was scaled to 500.
|
| |
|
| Submission date |
Jun 23, 2009 |
| Last update date |
Sep 16, 2009 |
| Contact name |
Tilahun Abebe |
| E-mail(s) |
Tilahun.Abebe@uni.edu
|
| Phone |
319-273-7151
|
| Organization name |
University of Northern Iowa
|
| Department |
Biology
|
| Street address |
191 McCollum Hall
|
| City |
Cedar Falls |
| State/province |
IA |
| ZIP/Postal code |
50614 |
| Country |
USA |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
| GSE16754 |
Comparative transcriptional profiling of organs of the barley spike |
|
