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Sample GSM71005 Query DataSets for GSM71005
Status Public on Sep 30, 2005
Title Col_Un4
Sample type RNA
 
Source name Whole Rossettes
Organism Arabidopsis thaliana
Characteristics Genotype: Columbia-0, wild-type; Treatment: untreated; Biological Replicate: 4 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).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the plants using a modified Trizol method (Chomczynski and Sashi, 1987) (see also Protocols Manual at the AFGC web page http://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/RevisedAFGC/AFGC_Protocols_Dec_2001L.pdf) and purified with a silica membrane column (Qiagen, RNeasy).
Label biotin
Label protocol 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 4 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.
 
Submission date Aug 18, 2005
Last update date Oct 28, 2005
Contact name Shauna Somerville
E-mail(s) shauna@andrew2.stanford.edu
Phone 650-325-1521
URL http://carnegiedpb.stanford.edu/research/research_ssomerville.php
Organization name Carnegie Institution of Washington
Department Plant Biology
Street address 260 Panama Street
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL198
Series (1)
GSE3220 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.

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE Normalized Ratio
AFFX-TrpnX-M_at 1.2 A 0.941556 N/A
AFFX-TrpnX-5_at 39.3 A 0.275146 N/A
AFFX-TrpnX-3_at 17.2 A 0.095667 N/A
AFFX-ThrX-M_at 17.3 A 0.5 N/A
AFFX-ThrX-5_at 2.2 A 0.760937 N/A
AFFX-ThrX-3_at 25 A 0.354453 N/A
AFFX-r2-P1-cre-5_at 17917.9 P 0.000244 1.0371175
AFFX-r2-P1-cre-3_at 19026 P 0.000244 1.0232397
AFFX-r2-Ec-bioD-5_at 3807.6 P 0.000244 1.1140926
AFFX-r2-Ec-bioD-3_at 4177.7 P 0.000244 1.1417869
AFFX-r2-Ec-bioC-5_at 992.4 P 0.000244 1.0999548
AFFX-r2-Ec-bioC-3_at 1232.6 P 0.000244 1.021803
AFFX-r2-Ec-bioB-M_at 478.2 P 0.000244 1.1207781
AFFX-r2-Ec-bioB-5_at 409.3 P 0.000732 1.2977779
AFFX-r2-Ec-bioB-3_at 470.1 P 0.000244 1.1830001
AFFX-r2-Bs-thr-M_s_at 8 A 0.753906 N/A
AFFX-r2-Bs-thr-5_s_at 54.7 A 0.080566 N/A
AFFX-r2-Bs-thr-3_s_at 9.8 A 0.80542 N/A
AFFX-r2-Bs-phe-M_at 20.3 A 0.303711 N/A
AFFX-r2-Bs-phe-5_at 1.9 A 0.633789 N/A

Total number of rows: 22810

Table truncated, full table size 764 Kbytes.




Supplementary data files not provided

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