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Sample GSM73163 Query DataSets for GSM73163
Status Public on Mar 10, 2008
Title SAS1-HA vs WT. Replica 1
Sample type RNA
 
Channel 1
Source name untransformed plants
Organism Arabidopsis thaliana
Characteristics Total RNA was extracted from 3 weeks old leaves of WT Arabidopsis thaliana Col-0
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from 3-4 weeks old rosettes using the RNAeasy plant mini kit (Qiagen) and subjected to reverse transcription and amplified by in vitro transcription with t7 polymerase (Ambion).
Label CY5
Label protocol Amplified RNA products were subjected to reverse transcription and then labeled with Cy3 and Cy5 by indirect amino-allyl method.
 
Channel 2
Source name SAS1-HA
Organism Arabidopsis thaliana
Characteristics Total RNA was extracted from 3 weeks old leaves of SAS1-HA over expression line in Arabidopsis thaliana Col-0
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from 3-4 weeks old rosettes using the RNAeasy plant mini kit (Qiagen) and subjected to reverse transcription and amplified by in vitro transcription with t7 polymerase (Ambion).
Label Cy3
Label protocol Amplified RNA products were subjected to reverse transcription and then labeled with Cy3 and Cy5 by indirect amino-allyl method.
 
 
Hybridization protocol For each biological repetition, two hybridizations with swapped dye labeling were preformed.
Scan protocol Separate images for each fluorescence were acquired using ScanArray 4000 software (Packard BioScience, Meridan, CT) at a resolution of 10 mm per pixel, adjusting the
photomultiplier and laser power to achieve an optimal distribution of
signals without minimal saturation.
Description RNA was extracted from plants that overexpress SAS1 and from non-transformed plants. Plants were grown for 3 weeks under long day conditions. Hybridization was performed on an array from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K Arabidopsis ESTs. Data in this platform contains 6 repetitions including 2 independent biological experiments.
Data processing Data analysis was performed applying per-spot
and per-chip normalization (GeneSpring 5.1; Silicon Genetics, Redwood
City, CA).
 
Submission date Sep 04, 2005
Last update date Mar 10, 2008
Contact name Robert Fluhr
E-mail(s) robert.fluhr@weizmann.ac.il
Phone 972-8-9342175
Organization name Weizmann Institute of Science
Department Plant Sciences
Street address
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL242
Series (1)
GSE3246 A serpin, SAS1, controls hormonal cross talk in the plant defense pathway

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (SAS1-HA/WT)
CH1 lowess normalized WT signal
CH2 lowess normalized SAS1-HA signal
PRE_VALUE Normalized ratio (SAS1-HA/WT)

Data table
ID_REF VALUE CH1 CH2 PRE_VALUE
3796
11492
2249
4958
10947
1152
11841
9663
1858
2945
3840
10140
384
6067 -0.1844 89.75 79.09 0.88
5300 0.0426 815.2 844.9 1.03
2997 -0.5995 6,969.87 4,636.69 0.66
2230 -1.8365 4,922.67 1,420.95 0.28
2998 0.4005 2,794.97 3,690.38 1.32
2231 -0.1361 7,639.18 7,006.43 0.91
2999 -0.0740 455.2 436.7 0.95

Total number of rows: 11965

Table truncated, full table size 383 Kbytes.




Supplementary file Size Download File type/resource
GSM73163.txt.gz 1.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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