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Sample GSM315457 Query DataSets for GSM315457
Status Public on Mar 02, 2009
Title Arabidopsis pGL1::GL1-GR with Dex treatment for 4 hours, sample 2
Sample type RNA
 
Source name Arabidopsis green tissues, pGL1::GL1-GR with Dex treatment for 4 hours, sample 2
Organism Arabidopsis thaliana
Characteristics GR inducible system using transgenic Arabidopsis carrying pGL1::GL1-GR
Extracted molecule total RNA
Extraction protocol RNA was extracted with Qiagen RNeasy Plant RNA extraction kit.
Label Biotin
Label protocol Following confirmation of RNA quality, Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) is used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA is synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA is achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA is purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content is measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
 
Hybridization protocol For each array, 2.2 µg of cDNA is hybridized onto Arabidopsis ATH1 Genome GeneChips® (Affymetrix Inc., USA), designed in collaboration with TIGR, containing more than 22,500 probe sets representing approximately 24,000 genes. The array is based on information from the international Arabidopsis sequencing project that was formally completed in December, 2000. In parallel and subsequent to the genome's completion, TIGR reannotated the entire genome in a project funded by the National Science Foundation and the resulting data was used in the design of this array. Hybridization is allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
Scan protocol GeneChips are scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA) and CEL files are generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals are generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and are used to determine differential gene expression by pair-wise comparisons. The genes that are altered by two-fold either way are sorted and used for further interpretation of the microarray data.
Description This experiment was done to compare the gene expression between Dex and mock treatment plants
Data processing AffyGUI, normalized by GCRMA.
 
Submission date Aug 26, 2008
Last update date Aug 28, 2018
Contact name Kengo Morohashi
E-mail(s) morohashi.1@osu.edu
Phone 614-688-4954
Organization name The Ohio State University
Department Molecular Genetics
Lab Erich Grotewold
Street address 1060 Carmack Rd
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
 
Platform ID GPL198
Series (1)
GSE12551 Inducible expression of trichome regulators, GL1 and GL3
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE GCRMA normalized signal intensity

Data table
ID_REF VALUE
244901_at 7.273380109
244902_at 6.361410697
244903_at 9.452626564
244904_at 2.118223727
244905_at 2.113679429
244906_at 5.357554056
244907_at 2.125092939
244908_at 2.112339313
244909_at 2.155266241
244910_s_at 3.717930109
244911_at 2.124396137
244912_at 7.622496171
244913_at 2.119206926
244914_at 2.484374762
244915_s_at 2.111584418
244916_at 2.108954367
244917_at 2.10980467
244918_at 2.117997979
244919_at 2.166547931
244920_s_at 6.971053765

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM315457.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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