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Rice 57K Affymetrix GeneChip Test

Experiment Name: Rice 57K Affymetrix GeneChip Test
Accession No. & GeneChip: OS1, Rice
Submitter: Experimenter: Timothy Close, submitted by Lishuang Shen
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: 2005-03-21 09:21:51
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: It is six replicates of Pokkali seedling RNA, three at one level of spiked control and three at another level. The "present" call rate is 45% for this indica rice RNA. The data were produced at the UC Irvine DNA and Protein Microarray Facility by Sriti Misra from RNA samples produced by my student Harkamal Walia at UC Riverside in a collaborative project with Clyde Wilson at the George E. Brown Jr. USDA Salinity Laboratory and Abdel Ismail at International Rice Research Institute. You may redistribute this now-public data as you wish, but please cite the source.


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 1.8pM final concentration of spikes.
This is enough for 3 arrays, can put 190ul of hyb cocktail per array.

For HighSpike, Make final cocktail at 3.6 pM final concentration of spikes
This is enough for 3 arrays, can put 190ul of hyb cocktail per array

Step 3. Hybridization.
Providers:
Name: Dr. Timothy Close
Institution: University of California, Riverside
Head of Laborotary: Dr. Timothy Close
email:
timothy.close@ucr.edu
Homepage:
http://plantbiology.ucr.edu/people/?Close&show;_for=new_window

 
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