|
| Status |
Public on Jan 22, 2009 |
| Title |
kara_with_aphids_1 |
| Sample type |
RNA |
| |
|
| Source name |
Barley variety Kara leaves with aphids
|
| Organism |
Hordeum vulgare |
| Characteristics |
Strain: Kara
Susceptible to R. padi
First leaf
Biological replicate 1
|
| Biomaterial provider |
Svalöf Weibull AB, Sweden
|
| Treatment protocol |
Seven days after seedlings were planted into soil, 20 aphids (mixed instars) per plant were put in a cage on the first leaf. Plants were kept at a 16/8 hr photoperiod, 160 µmol/m2s and a temperature of 20° C. After 48 hr aphids were removed from the plants and the piece of leaf in the cage was cut out and snap-frozen in liquid nitrogen. Each biological replicate consisted of 6 leaf pieces (the part of the leaf that was enclosed in the tube).
|
| Growth protocol |
Barley seeds were germinated in Petri dishes on filter paper moistened with 0.75 % hydrogen peroxide in water. After 3 days at 4° C in darkness, seeds were kept at room temperature for 2 days. Seedlings were then planted individually in pots with commercial potting mix. Seedlings were grown in a growth chamber at a 16/8 hr photoperiod, 160 µmol/m2s and a temperature of 20° C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 0.6 to 0.8 g (fresh weight) leaf tissue per sample using the Concert™ Plant RNA Reagent (Invitrogen) according to the large-scale protocol. This extraction was immediately followed by an additional purification step using the Qiagen RNeasy kit (Qiagen) following the RNA clean up protocol, including an on-column DNase treatment, according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
|
| |
|
| Hybridization protocol |
We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.
|
| Scan protocol |
We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.
|
| Description |
Analysis of changes in transcript accumulation in four different barley genotypes in response to aphid infestation. To avoid allelobiotic effects between different barley genotypes, the experiment was performed with only one line at a time and to avoid induction of defence responses in control plants by volatiles emitted from aphid-infested plants, control and infested plants were kept in separate growth chambers. The experiment was performed twice, separately with each plant genotype, and chambers were swapped between experiments. Three plants from each experiment were combined in each replicate.
|
| Data processing |
The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.
|
| |
|
| Submission date |
Aug 11, 2008 |
| Last update date |
Jan 22, 2009 |
| Contact name |
Gabriele Delp |
| E-mail(s) |
gabriele.delp@sh.se
|
| Phone |
+4686084704
|
| Organization name |
Södertörns University College
|
| Department |
Life Sciences
|
| Street address |
Alfred Nobels allé 7
|
| City |
Huddinge |
| ZIP/Postal code |
141 89 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
| GSE12584 |
Microarray analysis of the interaction between Rhopalosiphum padi and partially resistant or susceptible barley lines |
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