|
| Status |
Public on Mar 27, 2012 |
| Title |
Bgh at 24 hpi, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
24 hours post inoculation with B. graminis f. sp. hordei
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbare
protocol: inoculated with B. graminis f. sp. hordei (Bgh)
test: treated sample
tissue: rice leaf
|
| Treatment protocol |
Two week-old rice plants were inoculated with Bgh conidia by shaking inoculated barley plants over test plants in a settling tower of approximately 60 X 60 X 60 cm, in analogy to barley plants inoculation as previously described by Zellerhoff et al. (2010). Inoculations were done 1 to 2 h after the onset of light at an average density of 10 conidia mm leaf area. Control plants were left nontreated. Control and inoculated plants were incubated at a constant temperature of 20 °C and natural daylight (no direct sunlight) until RNA extraction.
|
| Growth protocol |
Plants grown in a glasshouse under a day-time temperature of 27°C, a night-time temperature of 22°C and 60% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each biological replicate was purified, using the TRIZOL protocol (Invitrogen, Carlsbad, CA), following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotin-labelled cRNA targets obtained by direct in vitro transcription reaction.
|
| |
|
| Hybridization protocol |
Following fragmentation, 8 ug of cRNA were hybridized according to the GeneChip standard protocol (Eukaryotic Target Preparation, Affymetrix) on the GeneChip® Rice Genome Array.
|
| Scan protocol |
According to the GeneChip standard protocol (Eukaryotic Target Preparation, Affymetrix) using GeneArray® Scanner at the excitation wavelength of 488 nm.
|
| Description |
gene expression data from rice leaf sample inoculated with B. graminis f. sp. hordei (Bgh)
|
| Data processing |
The data were analysed in R 2.12.0 applying the RMA algorithm from affy package. The default settings for all normalization procedures were used as implemented in the BioConductor.
|
| |
|
| Submission date |
Jul 26, 2011 |
| Last update date |
Mar 27, 2012 |
| Contact name |
PAMELA ABBRUSCATO |
| E-mail(s) |
pamela.abbruscato@tecnoparco.org
|
| Phone |
+3903714662623
|
| Fax |
+3903714662217
|
| URL |
http://www.tecnoparco.or/ricegenomics
|
| Organization name |
PARCO TECNOLOGICO PADANO
|
| Department |
RICE GENOMICS UNIT
|
| Street address |
via Einstein
|
| City |
LODI |
| State/province |
LO |
| ZIP/Postal code |
26900 |
| Country |
Italy |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE30942 |
Rice gene global expression during nonhost interaction with Blumeria graminis f. sp. hordei (Bgh) |
|
