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Sample GSM41202 Query DataSets for GSM41202
Status Public on May 24, 2005
Title det2_Mock2
Sample type RNA
 
Source name Genotype: Columbia-0, det2 mut.; Treatment: incubated with 80 percent ethanol for 3 hours; Biological Replicate: 2 of three
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Description Growth Conditions and Treatments: Arabidopsis thaliana seeds were surface sterilized. Approximately 15000 seeds(300 milligrams) were placed in a 1 L erlenmeyer flasks containing 300 mL of liquid Murashige and Skoog medium (Sigma, St Louis, MO, USA) containing 1.5% sucrose. These flasks were incubated with gentle shaking for 5 days under constant illumination at 22ºC. After this time, 15 ul of 80% ethanol was added as the mock control (BL treated received 15 ul of 2uM Brassinolide (BL) dissolved in 80% ethanol. The BL treatment results were not used and are thus not reported). Flasks were incubated for 3 hours with the ethanol. Whole seedlings from each treatment were collected, the medium was drained, and the seedlings were rapidly forzen in liquid nitrogen. The experiment was done alongside two other genetic backgrounds (wildtype and bzr1-1D) and was repeated three times (experiments 1-3) during different weeks.
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 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. To remove chip-to-chip and experiment-to-experiment signal variation each array was normalized by the intensity values of the top 50th percentile of genes on this array. The individual detection values were then normalized to the corresponding detection values of the wildtype (Colombia-0) control for each experiment. The normalized values for the data set are reported along with the intensity values for this array.
Keywords = Arabidopsis, hormone, brassinosteroid, det2, bzr1-1D
Lot batch = 510690
 
Submission date Feb 03, 2005
Last update date Oct 28, 2005
Contact name Joshua Martin Gendron
E-mail(s) jgendron@stanford.edu
Phone (650)325-1521
Organization name Carnegie Institution of Washington/Stanford University
Department Plant Biology
Lab Wang
Street address 260 Panama Rd.
City Stanford
State/province CA
ZIP/Postal code 94037
Country USA
 
Platform ID GPL198
Series (1)
GSE2696 Brassinosteroid mutant (bzr1-1D and det2) analysis

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 Value of Control A normalized measurement of control arrays for each probe set calculated in GeneSpring 4.2.

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE Normalized Value of Control
244901_at 177.1 P 0.00293 1.109892368
244902_at 249.1 P 0.000244 1.788343906
244903_at 397.6 P 0.00415 1.411064506
244904_at 15.7 A 0.398926 0.527656853
244905_at 61.3 A 0.5 0.479506582
244906_at 380.8 P 0.01416 1.269408345
244907_at 47.1 A 0.27417 0.957636774
244908_at 3.2 A 0.969727 1.099763989
244909_at 98.3 A 0.334473 1.318998218
244910_s_at 86.1 P 0.000244 2.79666543
244911_at 5.6 A 0.601074 0.259400845
244912_at 1668.3 P 0.001221 1.354726076
244913_at 96.7 A 0.633789 1.174730062
244914_at 3.4 A 0.780518 1.131983519
244915_s_at 34.8 A 0.633789 0.461141676
244916_at 19.6 A 0.567627 0.962293446
244917_at 5.9 A 0.753906 1.208815098
244918_at 11.1 A 0.398926 0.47493574
244919_at 65.6 A 0.246094 4.754421234
244920_s_at 505.2 P 0.000732 1.210067987

Total number of rows: 22810

Table truncated, full table size 855 Kbytes.




Supplementary data files not provided

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