Difference between revisions of "Dbashour Week 12"
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==Outline of Article== | ==Outline of Article== | ||
| − | + | ===Background Information on Purpose of Experiment=== | |
* Low temperatures are known to have several effects on biochemical and physiological properties in various cells | * Low temperatures are known to have several effects on biochemical and physiological properties in various cells | ||
* Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment | * Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment | ||
| − | * In yeast, the NSR1, TIP1, and OLE1 genes have been identified as important cold-inducible genes through past research | + | * In yeast, the NSR1, TIP1, and OLE1 genes have been identified as important cold-inducible genes through past research |
| − | * The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells | + | *low temperature-dependent gene expression and low temperature response are still unclear |
| − | + | * '''The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells''' | |
| − | * | + | ===Cold shock and microarray procedures of yeast samples=== |
| − | * | + | * S. cerevisiae YPH500 was used for all the analyses |
| − | * | + | * Cultured aerobically in YPD medium (yeast extract, peptone, and glucose) at 30°C and shaken at 100 rpm |
| − | * | + | * 50 ml of the culture were collected for a reference time of 0 |
| + | * Cells flash-frozen in liquid nitrogen | ||
| + | * Stored at -80°C in preparation for RNA | ||
| + | * The remaining cells were cold shocked at 10°C then cultured at the same temperature | ||
| + | * Cells collected at 0.25, 0.5, 2, 4, and 8 hours after the cold shock | ||
| + | * Cells flash-frozen in liquid nitrogen | ||
| + | * Stored at -80°C in preparation for RNA | ||
| + | * Cy3-dUTP and Cy5-dUTP were used as cDNA probes | ||
| + | * Labeled with fluorophore in order to carry out microarray hybridization | ||
| + | *Microarray hybridization performed based on the manual for S. cerevisiae cDNA microarray | ||
| + | * Microarrays were scanned by laser microscope | ||
| + | * Process repeated twice | ||
| + | * Averaged the expression ratios of the separate experiments for final data | ||
| + | * Images analyzed by computer program | ||
| + | * Data analyzed by analysis software | ||
| + | * Fluorescence intensities were normalized | ||
| + | * Data was clustered and referred to the Munich Information Center for Protein Sequences functional database | ||
| + | *functional relationships among the genes in each cluster was determined | ||
III. Results and Discussion | III. Results and Discussion | ||
* | * | ||
Revision as of 09:16, 21 November 2017
Contents
Article
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
List of 10 Unknown Words and Their Definitions
Outline of Article
Background Information on Purpose of Experiment
- Low temperatures are known to have several effects on biochemical and physiological properties in various cells
- Cold shock proteins are induced when cells are exposed to low temperatures in order to cope with the drastic change in environment
- In yeast, the NSR1, TIP1, and OLE1 genes have been identified as important cold-inducible genes through past research
- low temperature-dependent gene expression and low temperature response are still unclear
- The purpose of this experiment is to analyze global gene expression in low temperature-exposed yeast cells using a yeast cDNA microarray to obtain fundamental information on low temperature response and low temperature-dependent gene expression in yeast cells
Cold shock and microarray procedures of yeast samples
- S. cerevisiae YPH500 was used for all the analyses
- Cultured aerobically in YPD medium (yeast extract, peptone, and glucose) at 30°C and shaken at 100 rpm
- 50 ml of the culture were collected for a reference time of 0
- Cells flash-frozen in liquid nitrogen
- Stored at -80°C in preparation for RNA
- The remaining cells were cold shocked at 10°C then cultured at the same temperature
- Cells collected at 0.25, 0.5, 2, 4, and 8 hours after the cold shock
- Cells flash-frozen in liquid nitrogen
- Stored at -80°C in preparation for RNA
- Cy3-dUTP and Cy5-dUTP were used as cDNA probes
- Labeled with fluorophore in order to carry out microarray hybridization
- Microarray hybridization performed based on the manual for S. cerevisiae cDNA microarray
- Microarrays were scanned by laser microscope
- Process repeated twice
- Averaged the expression ratios of the separate experiments for final data
- Images analyzed by computer program
- Data analyzed by analysis software
- Fluorescence intensities were normalized
- Data was clustered and referred to the Munich Information Center for Protein Sequences functional database
- functional relationships among the genes in each cluster was determined
III. Results and Discussion
IV. Conclusion
V. Further Implications
Deliverable
Journal Club Week 12 Presentation
