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Sample GSM39197 Query DataSets for GSM39197
Status Public on Sep 30, 2005
Title RRE1_Chitin3
Sample type RNA
 
Source name chitin treated mutant rre1-1 seedlings. (biological replicate: 3 of 4)
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Description Genotype: rre1-1 (rapid response to elicitor 1-1), a T-DNA insertion mutant (SALK_066755). RRE1 (At2g35000) enocdes a protein with a RING domain found in ubiqitin E3 ligases. Treatment: incubated with hydrolyzed crab-shell chitin for 30 minutes.
Growth Conditions and Treatments: All experiments were performed as previously described (Ramonell et al., 2002, Mol. Plant. Pathol. 3(5), 301-311). Arabidopsis thaliana seeds were surface sterilized. Approximately 500 seeds (10 micrograms) were placed in 250 mL Erlenmeyer flasks containing 125 mL of liquid Murashige and Skoog medium (Sigma, St Louis, MO, USA) containing 2% dextrose. These flasks were incubated with gentle shaking for 14 days under constant illumination (125 µEinsteins m-2 s-1) at 22ºC. Acid-hydrolysed, crab-shell chitin (Sigma, St Louis, MO, USA) was added to give a final concentration 100 mg/L. The control flasks received an equivalent amount of sterile, double-distilled water for each treatment. Flasks were incubated for 30 minutes with the crab-shell chitin. Whole seedlings from each treatment were collected, the medium was drained, and the seedlings were rapidly forzen in liquid nitrogen. The results of four replicates are presented.
RNA and Microarray Methods: 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). Fifteen micrograms biotinylated complementary RNA (cRNA) was prepared and used to hybridize ATH1 Arabidopsis GeneChips (Affymetrix) using the Affymetrix manufacturer’s protocols. 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.
Keywords = chitin, defense, elicitor, mutant, PAMP, protein degradation, ring zinc finger protein, ubiquitin E3 ligase
Lot batch = 510690
 
Submission date Jan 19, 2005
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)
GSE2169 rre1 and rre2 mutants
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

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 idendifier 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-BioB-5_at 191.2 P 0.00141 0.7987474
AFFX-BioB-M_at 196.1 P 0.00007 0.99473876
AFFX-BioB-3_at 150.6 P 0.00011 0.8022971
AFFX-BioC-5_at 655.8 P 0.000052 1.0160121
AFFX-BioC-3_at 557.8 P 0.000095 1.2755693
AFFX-BioDn-5_at 1012.1 P 0.000052 1.255679
AFFX-BioDn-3_at 1646.7 P 0.000044 0.8158668
AFFX-CreX-5_at 5201.1 P 0.000044 0.9098302
AFFX-CreX-3_at 7870.9 P 0.000044 0.9456509
AFFX-DapX-5_at 7.3 A 0.544587 0.28667882
AFFX-DapX-M_at 16 A 0.327079 1.2592436
AFFX-DapX-3_at 8 A 0.868639 2.754584
AFFX-LysX-5_at 1.9 A 0.941556 0.3298179
AFFX-LysX-M_at 5.3 A 0.953518 1.630038
AFFX-LysX-3_at 23.7 A 0.102165 5.4233627
AFFX-PheX-5_at 3.2 A 0.966323 1.062834
AFFX-PheX-M_at 2.7 A 0.712257 0.84196234
AFFX-PheX-3_at 28.8 A 0.262827 1.8597845
AFFX-ThrX-5_at 11.8 A 0.712257 2.1342595
AFFX-ThrX-M_at 23.7 A 0.131361 2.2989929

Total number of rows: 22810

Table truncated, full table size 814 Kbytes.




Supplementary file Size Download File type/resource
GSM39197.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM39197.CHP.gz 5.7 Mb (ftp)(http) CHP
GSM39197.EXP.gz 481 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data provided as supplementary file

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