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Sample GSM311257 Query DataSets for GSM311257
Status Public on Jan 22, 2009
Title hsp5_without_aphids_2
Sample type RNA
Source name Barley variety Hsp5 leaves without aphids
Organism Hordeum vulgare subsp. spontaneum
Characteristics Strain: Hsp5
Partially resistant to R. padi
First leaf
Biological replicate 2
Biomaterial provider Svalöf Weibull AB, Sweden
Treatment protocol Seven days after seedlings were planted into soil, empty cages were put on their first leaf (no-aphid control). Plants were kept at a 16/8 hr photoperiod, 160 µmol/m2s and a temperature of 20° C. After 48 hr cages 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
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

Data table header descriptions
VALUE MAS5-calculated signal intensity
ABS_CALL Call in an absolute analysis that indicates if the signal was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value of the detection call

Data table
AFFX-BioB-5_at 85.8522 P 0.00159257
AFFX-BioB-M_at 65.6081 P 0.000753643
AFFX-BioB-3_at 55.4178 P 0.000509415
AFFX-BioC-5_at 229.295 P 7.00668e-05
AFFX-BioC-3_at 232.36 P 4.42873e-05
AFFX-BioDn-5_at 295.504 P 4.42873e-05
AFFX-BioDn-3_at 1058.56 P 6.02111e-05
AFFX-CreX-5_at 2265.05 P 4.42873e-05
AFFX-CreX-3_at 3598.76 P 5.16732e-05
AFFX-DapX-5_at 39.0566 P 0.002867
AFFX-DapX-M_at 85.7511 P 0.0020226
AFFX-DapX-3_at 202.899 P 0.000126798
AFFX-LysX-5_at 14.613 A 0.116113
AFFX-LysX-M_at 21.0258 A 0.262827
AFFX-LysX-3_at 42.487 P 0.0012475
AFFX-PheX-5_at 10.3855 A 0.195266
AFFX-PheX-M_at 15.6076 A 0.41138
AFFX-PheX-3_at 46.1155 P 0.0166701
AFFX-ThrX-5_at 18.559 A 0.205712
AFFX-ThrX-M_at 30.4285 P 0.00933744

Total number of rows: 22840

Table truncated, full table size 784 Kbytes.

Supplementary file Size Download File type/resource
GSM311257.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM311257.CHP.gz 125.4 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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