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| Status |
Public on Nov 01, 2008 |
| Title |
WildType_Rep_3 |
| Sample type |
RNA |
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| Source name |
Wild Type
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Strain: Wild Type
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| Growth protocol |
Each strain was inoculated in 1 mL SDC and grown overnight. Saturated overnight cultures were then diluted into 3 flasks each containing 50 mL of culture. All samples were incubated at 30°C with shaking (2200 rpm) until day 2.5. In the SDC medium, a substantial proportion of yeast cells are still dividing before day 2. At older ages, such as day 3–5, most of the cells become hypometabolic, which is associated with a dramatic drop in transcription. We harvest mRNA at day 2.5 so that we can extract enough mRNA for microarray experiment while avoid the noise introduced by the transcriptional activities of dividing cells.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from day 2.5 post-diauxic yeast cultures (2.0×108 cells) according to the acid phenol protocol. Briefly, yeast were collected by centrifugation, washed with cold water once, and resuspended in 400 µl of 10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS. After adding 400 µl of warm acid phenol the cell suspension was incubated at 65°C for 20 minutes with vortexing every 5 minutes, centrifuged and the supernatant extracted twice with acid phenol and once with chloroform. Total RNA was recovered by precipitation with ethanol and cleaned up by using the RNAsy kit (Qiagen). RNA (5 µg/sample) was sent to the UCLA DNA array Core Facility.
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| Label |
biotin
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| Label protocol |
Done by UCLA DNA array Core Facility; http://microarray.genetics.ucla.edu/
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| Hybridization protocol |
Done by UCLA DNA array Core Facility; http://microarray.genetics.ucla.edu/, The biotin-labeled cRNA was hybridized to Affymetrix GeneChip® Yeast2.0 Array.
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| Scan protocol |
Done by UCLA DNA array Core Facility; http://microarray.genetics.ucla.edu/
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| Description |
Microarray Experiment is done in UCLA DNA array Core Facility
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| Data processing |
The normalization is carried out in a pairwise fashion. Namely, for each wild type sample (W1, W2, W3), three replicates of a mutant are normalized with respect to each reference. Take sch9Δ (triplicates: S1, S2 and S3) or example, the normalized arrays with respect to W1, W2, W3 are respectively denoted by S1\W1, S2\W1, S3\W1, S1\W2, S2\W2, S3\W2, S1\W3, S2\W3, S3\W3. We group the wild type and normalized mutant arrays by the reference, and then summarize each group. Take sch9Δ for example. We summarize the four arrays (the reference plus three normalized) W1, S1\W1, S2\W1, S3\W1 together. This leads to three estimates of expression fold changes of the mutant versus the wild type. In total, we have nine estimates from three wild type references, and we take their median difference as the final estimate. The details for this pre-processing can be found in [Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, et al. (2007) Significant and Systematic Expression Differentiation in Long-Lived Yeast Strains. PLoS ONE 2(10): e1095. doi:10.1371/journal.pone.0001095]
Signal estimates for individual samples were not generated by the analysis. See the Series record for expression fold change estimates.
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| Submission date |
Oct 31, 2008 |
| Last update date |
Oct 31, 2008 |
| Contact name |
Huanying Ge |
| E-mail(s) |
hge@usc.edu
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| Organization name |
Computational biology and bioinformatics
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| Department |
Biology
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| Lab |
Lei Li
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| Street address |
1050 Childs Way, RRI building 408D
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL2529 |
| Series (1) |
| GSE13420 |
Significant and Systematic Expression Differentiation in Long-Lived Yeast Strains |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM338562.CEL.gz |
1.6 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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