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Wheat GeneChip Test | |||||||||||
| Experiment Name: | Wheat GeneChip Test | ||||||||||
| Accession No. & GeneChip: | TA2, Wheat | ||||||||||
| Submitter: | Timothy J Close | ||||||||||
| Experiment Type: | dose response | ||||||||||
| Experiment Factor: | dose | ||||||||||
| Number of Replicates: | 3 | ||||||||||
| Quality Control Steps: | biological replicates technical replicates | ||||||||||
| Quality Control Description: | None | ||||||||||
| Publication_id: | None | ||||||||||
| Last Update Time: | 2005-02-25 16:35:18 | ||||||||||
| Expression Data Access & Analysis: | Please select one action: 1. Batch download all data files at Download Center . 2. Browse Hybridizations and boxplots from experiment. 3. Visualization of hybridizations or treatment means with scatterplots and MvA plots. 4. Browse Samples from experiment. 5. Create Gene List by filter probe sets for differentially-expressed genes. 6. Pattern Recognition on filtered gene list. | ||||||||||
| Description: | One RNA sample was used. The RNA source material was Chinese Spring wheat whole seedling minus starchy endosperm. Equal portions of RNA from unstressed and 48 hr drought-stressed seedling were combined to make one RNA sample. The person who produced the RNA was Rehana Asghar in the TJ Close lab at University of California, Riverside. Everything downstream of RNA production was done at the UC Irvine DNA and Protein Microarray Facility (Denis Heck, manager) by Sriti Misra. One batch of labeled cRNA was produced. It was divided in half, each half receiving a different amount of spike, provided by Gene Tanimoto of Affymetrix. Each half was then distributed to three chips to test chip-chip variation. Step 1. Prepare master mix of hyb cocktail with enough room to add spikes, and water to adjust final volume: 60 ug cRNA sample 1 In hyb cocktail w/o spikes Enough for 6 arrays Step 2. For LowSpike, Make final cocktail at 1.5pM final concentration of spikes. This is enough for 3 arrays, can put 190ul of hyb cocktail per array. For HighSpike, Make final cocktail at 3.0 pM final concentration of spikes This is enough for 3 arrays, can put 190ul of hyb cocktail per array Step 3. Hybridization. | ||||||||||
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