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Sample GSM6572 Query DataSets for GSM6572
Status Public on Aug 15, 2003
Title CU1
Sample type RNA
Source name Genotype: Columbia-0, wild-type; Treatment: uninoculated; Biological Replicate: 1 of four
Organism Arabidopsis thaliana
Extracted molecule total RNA
Description Growth Conditions and Inoculations: All experiments were performed as previously described (Vogel and Somerville, 2000, Proc. Natl. Acad. 97: 1897-1902). Arabidopsis thaliana and Hybrid Kuta squash (Park Seed, Greenwood, SC) were grown in growth chambers at 22o C with a 14 hr photoperiod and a light intensity of approximately 125 µEinsteins m-2 s-1 provided by Phillips F32T8 fluorescent lamps. Powdery mildew (Erysiphe cichoracearum UCSC1) was cultured on squash for 10-12 days and was then applied to Arabidopsis using 1.3 m settling towers. Plants were 3 weeks old at the time of inoculation.
RNA and Microarray Methods: Total RNA was extracted from the plants using the Trizol method (Invitrogen, Ramonell et al. (2002) Mol. Plant Pathol. 3: 301) and purified with a silica membrane column (Qiagen, RNeasy). Twenty micrograms biotinylated complementary RNA (cRNA) was prepared as described (Hernan et al. (2003) Cancer Res. 63, 140) from the purified total RNA. The resulting cRNA was used to hybridize ATH1 Arabidopsis GeneChips (Affymetrix) using the manufacturer’s protocols. The array images were analyzed with the Affymetrix Microarray Suite 5.0 software with the target intensity set to 500. These data were imported into GeneSpring 4.2. To remove chip-to-chip signal variation, the reference data set, consisting of the intensity values for each gene averaged over four replicates of Columbia-1, uninoculated, was normalized by the intensity values of the top 50th percentile of genes on this array. The normalized values for the reference data set (Normalized Value of Control) are reported along with the intensity values for this array.
Keywords = callose, defense, disease, host-pathogen interaction, mutant, powdery mildew, salicylic acid
Lot batch = 1000854
Submission date May 12, 2003
Last update date Aug 28, 2018
Contact name Shauna Somerville
Phone 650-325-1521
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)
GSE431 pmr4 vs. wild-type (May, 2003)
Reanalyzed by GSE119083

Data table header descriptions
ID_REF As defined by Affymetrix, these are the probe set identifiers, each of which is unique to a specific probe set defining a specific region of a single 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 Value of Control A normalized measurement of control arrays for each probe set calculated in GeneSpring 4.2
Shown on the paper A symbol indicating if the probe set is shown on the paper (Y), or not shown on the paper (N)

Data table
ID_REF VALUE ABS_CALL Detection p-value Normalized Value of Control Shown on the paper
245016_at 3732 P 0.000244 3479.882 N
261585_at 32.2 A 0.432373 57.401 N
261568_at 25.3 A 0.533936 24.339 N
261584_at 255.1 A 0.095215 255.987 N
261579_at 1825.4 P 0.000732 2066.167 N
261569_at 125 P 0.001953 188.185 N
261576_at 199.6 P 0.008057 192.978 N
261577_at 2070 P 0.000244 2252.53 N
261583_at 4840.2 P 0.000244 5141.025 N
261578_at 6805.2 P 0.000244 7220.829 N
261580_at 4.9 A 0.665527 20.575 N
261570_at 683.1 P 0.000732 608.297 N
261575_at 48.1 A 0.398926 43.689 N
261581_at 1151.3 P 0.000732 1221.436 N
261571_at 38.5 P 0.037598 37.668 N
261582_at 418.3 P 0.001221 454.244 N
261572_at 2928.5 P 0.000244 3718.388 N
261573_at 26 A 0.567627 64.385 N
261574_at 90.3 A 0.366211 130.118 N
261042_at 53.1 A 0.567627 64.085 N

Total number of rows: 22810

Table truncated, full table size 804 Kbytes.

Supplementary file Size Download File type/resource
GSM6572.CHP.gz 5.8 Mb (ftp)(http) CHP
GSM6572.RPT.gz 898 b (ftp)(http) RPT
GSM6572.cel.gz 3.3 Mb (ftp)(http) CEL
GSM6572.exp.gz 512 b (ftp)(http) EXP
Processed data provided as supplementary file

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