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Browse RicePLEX Experiment Data

Choose an experiment:
Rice 57K Affymetrix GeneChip Test
Timothy Close, University of California, Riverside (timothy.close@ucr.edu)
Experiment design (6 hybridizations)
dose
•HiSpike •LowSpike

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 ...[complete overview]

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Experiment Name: Rice 57K Affymetrix GeneChip Test
Accession No: OS1
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
dose
•HiSpike  •LowSpike
Quality Control: biological replicates
technical replicates
Treatment summary:
 dose  # replicates
 HiSpike  3
 LowSpike  3
Total hybridizations: 6
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.
Publication: none
Created: 2005-03-21 09:21:51
Last Update: 2008-08-05 12:12:23
Submitter: Lishuang Shen
Name: Timothy Close
Institution: University of California, Riverside
Head of Laboratory: Timothy Close
email(s):
Homepage:

 
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