|
| Status |
Public on Mar 11, 2011 |
| Title |
genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
phyllome (genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA)
|
| Organism |
Hordeum vulgare |
| Characteristics |
germplasm name: ci 16151 (mla6)
tissue: po: 0006001 phyllome
developmental stage: PO:0007134 A vegetative growth
age: 8.5 days at time of sampling
growth media: garden soil
|
| Growth protocol |
Growth Description: Plants were grown for 7 days in the greenhouse, then inoculated with Bgh isolate 5874, or non-inoculated and transferred to a growth chamber for 32 hours. They were then sampled. Environmental Conditions: Growth chamber:18C; 16hr light, 8hr night; relative humidity set to 65%
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up
|
| Label |
biotin
|
| Label protocol |
Affymetrix one-cycle target labeling
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Hyb
|
| Scan protocol |
Affy- Array Scanning
|
| Description |
This sample is of either the incompatible genotype CI 16151 (Mla6), or compatible genotype CI 16151 m9472 (mla6). Following 7 days of germination the sample was either inoculated with Bgh isolate 5874 (AVRa6), or noninoculated. 32 hours after infection tissue was harvested. From this tissue either total RNA or polysomal RNA was isolated for hybridization.
|
| Data processing |
The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.
|
| |
|
| Submission date |
Feb 11, 2010 |
| Last update date |
Mar 11, 2011 |
| Contact name |
PLEXdb Curator, Sudhansu Dash |
| Organization name |
Iowa State University
|
| Department |
Virtual Reality Application Center
|
| Lab |
PLEXdb
|
| Street address |
1023 Crop Genomes Informatics Lab (Iowa State University)
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
| GSE20279 |
Blumeria graminis fsp hordei effects on translation initiation in compatible and incompatible barley |
|
