NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6577 Query DataSets for GSM6577
Status Public on Aug 15, 2003
Title PI1
Sample type RNA
 
Source name Genotype: pmr4-1, callose synthase deficient mutant; Treatment: 3 days after inoculation with powery mildew; 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
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)
GSE431 pmr4 vs. wild-type (May, 2003)
Relations
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 2137.3 P 0.000244 3397.834 N
261585_at 141.9 A 0.219482 56.048 N
261568_at 21.4 A 0.432373 23.765 N
261584_at 303.2 P 0.030273 249.951 N
261579_at 2562.3 P 0.000732 2017.452 N
261569_at 134.8 P 0.030273 183.748 N
261576_at 200.2 P 0.00415 188.428 N
261577_at 2055.5 P 0.000244 2199.421 N
261583_at 4304.1 P 0.000244 5019.812 N
261578_at 7368.4 P 0.000244 7050.579 N
261580_at 7.1 A 0.665527 20.09 N
261570_at 579.6 P 0.000732 593.955 N
261575_at 23.4 A 0.665527 42.659 N
261581_at 1609.2 P 0.000732 1192.637 N
261571_at 21.4 A 0.080566 36.78 N
261582_at 428 P 0.001953 443.534 N
261572_at 3015.8 P 0.000244 3630.718 N
261573_at 81.8 A 0.067627 62.867 N
261574_at 95.3 A 0.27417 127.051 N
261042_at 7.2 A 0.665527 62.574 N

Total number of rows: 22810

Table truncated, full table size 803 Kbytes.




Supplementary file Size Download File type/resource
GSM6577.CHP.gz 5.8 Mb (ftp)(http) CHP
GSM6577.RPT.gz 904 b (ftp)(http) RPT
GSM6577.cel.gz 3.3 Mb (ftp)(http) CEL
GSM6577.exp.gz 507 b (ftp)(http) EXP
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap