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Sample GSM313028 Query DataSets for GSM313028
Status Public on Mar 02, 2009
Title Arabidopsis green tissue wild type L. er sample 1
Sample type RNA
Source name Arabidopsis green tissues 20 days old
Organism Arabidopsis thaliana
Characteristics Arabidopsis seedling, grown on MS medium for 20 days.
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 wild type seedlings and gl3egl3 double mutants.
Data processing Affy-GUI, normalized by GCRMA.
Submission date Aug 15, 2008
Last update date Aug 28, 2018
Contact name Kengo Morohashi
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)
GSE12522 Comparison of gene expression between wild type and gl3 egl3 trichomeless mutant green seedling tissues
Reanalyzed by GSE119083

Data table header descriptions
VALUE GCRMA normalized signal intensity

Data table
244901_at 7.290135248
244902_at 8.198400715
244903_at 9.104407926
244904_at 2.144075553
244905_at 2.171352703
244906_at 3.016054875
244907_at 2.202821543
244908_at 2.188272662
244909_at 2.172937411
244910_s_at 2.193431437
244911_at 2.246389453
244912_at 7.931682189
244913_at 2.214286408
244914_at 2.2513688
244915_s_at 2.17313946
244916_at 2.164246363
244917_at 2.179188777
244918_at 2.333984332
244919_at 2.526384794
244920_s_at 7.083929416

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.

Supplementary file Size Download File type/resource
GSM313028.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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