Genotype: Columbia-0, wild-type; Treatment: untreated; Biological Replicate: 2 of four
Biomaterial provider
Shauna Somerville Laboratory
Treatment protocol
Growth Conditions and Treatments: Three week-old wild-type Col and mutant pen3 Arabidopsis thaliana plants were inoculated with Erysiphe cichoracearum, Blumeria graminis hordei, or not inoculated. 1 day post inoculation 16 rosettes were harvested per replicate. 4 replicates were perfomerd per treatment.
Growth protocol
Plants were grown and inoculated as described (Nishimura et al., 2003, Science, 301, 969-972).
Fifteen micrograms biotinylated complementary RNA (cRNA) was prepared.
Hybridization protocol
Hybridizations to ATH1 Arabidopsis GeneChips (Affymetrix) were done using the Affymetrix manufacturer’s protocols.
Scan protocol
standard Affymetrix procedures
Description
Three week-old wild-type Col Arabidopsis thaliana plants, not inoculated. Replicate 2 of four.
Data processing
The array images were analyzed with the Affymetrix GeneChip Operating Software (GCOS) 1.1 with the target intensity set to 500. These data were imported into GeneSpring 7.0 (Silicon Genetics, Redwood City, CA, USA). To remove chip-to-chip signal variation, each measurement was divided by the 50.0th percentile of all measurements in that sample. All samples were normalized to the reference data set, consisting of four replicates of Columbia-0, untreated. Each measurement for each gene was divided by the median of that gene’s intensity in the reference data set. The normalized values (Normalized Ratio) are reported along with the intensity values for this array.
Arabidopsis pen3 mutant and wild type Col-O comparison under host inoculation, nonhost inoculation and no inoculation.
Data table header descriptions
ID_REF
As defined by Affymetrix, there are the probe set identifiers, each of which is unique to a specific probe set defining a specific reagion of a singal gene or set.
VALUE
This is the final calculated measurement for each probe set identifier that has been made comparable across all samples and rows.
ABS_CALL
A qualitative measurement indicating if the probe set is detected (Present; P), not detected (Absent; A), or marginally detected (Marginal;M)
DETECTION P-VALUE
A p-value indicating the significance of the Detection call. A Detection p-value measures the probability that the discrimination scores of all probe pairs in the probe set are above a certain level, and that the target is likely to be Present.
Normalized Ratio
A normalized ratio for each probe set calculated in GeneSpring 7.0 as described under Sample Description.
