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Sample GSM1329159 Query DataSets for GSM1329159
Status Public on Mar 18, 2014
Title WT-H2O2
Sample type RNA
 
Source name Yeast wild type cells without H2O2 treatment
Organism Saccharomyces cerevisiae
Characteristics strain: FM391
ploidy: Haploid
agent: none
Treatment protocol Cells were treated with 0.4 mM H2O2 for 20 min.
Growth protocol Cells were grown in yeast synthetic complete drop out (SC-Leu) medium at 30 °C on shaker to early log phase (OD600 ~0.4).
Extracted molecule total RNA
Extraction protocol Cells were resuspended in TES solution (10 mM Tris-HCl [pH 7.5], 10 mM EDTA, 0.5% SDS), and incubated with acidic phenol (pH 4.5; Sigma) for 1 hr at 65 °C. Samples were placed on ice for 10 min and centrifuged for 5 min at 13,000 rpm at 4 °C. Aqueous phases were extracted again with phenol and chloroform. RNA was precipitated in 100% ethanol for at least 2 h at -20 °C, centrifuged at 13,000 rpm for 15 min at 4°C, washed with 70% ethanol, and resuspended in water. Residual DNA was removed by DNase digestion using the RNase-Free DNase Set (Qiagen). RNA samples were further purified by RNeasy Kit (Qiagen).
Label Biotin
Label protocol RNA samples were amplified and reverse-transcribed using the NuGEN Ovation Pico WTA System V2 with 50ng RNA according to the manufacturer’s protocol. The yield of resulting cDNA was measured on the Caliper LabChip DS, and product sizing was evaluated on the Bioanalyzer. 5µg of each sample was fragmented and labeled with the Nugen Encore Biotin Module following the manufacturer’s protocol.
 
Hybridization protocol Samples were prepared for hybridization to the Affymetrix Yeast Genome 2.0 arrays using the Affymetrix GeneChip Hybridization, Wash and Stain Kit. Modifications were made to the Affymetrix protocol using the cocktail assembly for Mini Arrays. Samples were hybridized overnight in an Affymetrix GeneChip Hybridization Oven 640.
Scan protocol Samples were then processed on the GeneChip Fluidics Station 450 and GeneChip Scanner 3000 7G.
Description Gene expression data from early log phase of cells
Data processing Data were analyzed with Genesifter software, Analysis Edition (Perkin Elmer) for background correction and GC-RMA was used as the normalization method.
 
Submission date Feb 17, 2014
Last update date Mar 19, 2014
Contact name Chi Kwan Tsang
E-mail(s) [email protected]
Organization name Jinan University
Department Clinical Neuroscience Institute
Street address Building #3, 613 Huangpu avenue west
City Guangzhou
ZIP/Postal code 510630
Country China
 
Platform ID GPL2529
Series (1)
GSE55081 Expression data from yeast wild type (WT) and sod1Δ strains after treatment with hydrogen peroxide (H2O2)

Data table header descriptions
ID_REF
VALUE GC-RMA normalized data processed by Genesifter software, Analysis Edition

Data table
ID_REF VALUE
1769308_at 8.37177
1769309_at 2.17075
1769310_at 2.15863
1769311_at 11.1297
1769312_at 7.56079
1769313_at 7.6469
1769314_at 11.5111
1769315_at 2.08671
1769316_s_at 2.08917
1769317_at 10.4898
1769318_at 2.18078
1769319_at 9.77239
1769320_at 6.46481
1769321_at 10.4863
1769322_s_at 11.1983
1769323_at 8.38582
1769324_at 7.58238
1769325_at 5.22361
1769326_at 2.18367
1769327_at 2.22913

Total number of rows: 10928

Table truncated, full table size 203 Kbytes.




Supplementary file Size Download File type/resource
GSM1329159_Yeast_3_set2_WT_untreated.CEL.gz 916.7 Kb (ftp)(http) CEL
Processed data included within Sample table

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