UK MicroArray Core Facility

University of Kentucky, 156 Health Science Research Building, Lexington, KY 40536-0305

e-mail: dnachip@uky.edu

Contact: Ms. Donna Wall, Staff Analyst;  e-mail: dwall1@uky.edu    Phone: (859) 323-6979 Fax: (859) 257-9700 

Contact: Dr. Kuey-Chu Chen, Director;  e-mail: kueyc@uky.edu, phone: (859) 323-6241

[ Home ] [ Affymetrix GeneChip ] [ DNA array ] [ array RNA preparation ] [ Microarray Facility Pilot Program ] 

Custom cDNA Arrays

 A sample array from the Mouse 15K library shown in pseudo-colors.

Equipment:

1. Affymetrix 417 DNA Arrayer

For spotting DNA on nylon membranes or glass slides.  Currently configured to spot on nylon membranes. 

2. Affymetrix 428 Fluorescence Reader 

Quantification of hybridization of fluorescently tagged nucleic acids to DNA spotted on microscope slides.

3. MJ Research Tetrad Thermal Cycler  

 Amplfication of clones from plasmids in preparation for spotting.

4. Bioanalyzer 

Analysis of the quality of RNA samples.

Fee Services:

Gene Selection

The NIA 15K mouse gene set is available for use.           

1. Subsets of this gene set will be available for purchase.  Each subset is    approximately 1,000 genes.

2. Custom subsets of this gene set also may be designed by users.

3. Users also may elect to amplify their own gene sets and have them spotted.

Amplification of clones for spotting

1. Facility staff performs amplification of all gene sets owned by the facility.

2. User owned gene sets will be amplified by the user.  All amplified DNA must be prepared in a 96-well plate format in plates approved by the core facility.  Access to the MJ Research Thermal cycler must be scheduled in advance.

Spotting Service 

All spotting with the Affymetrix 417 Arrayer is done by core facility staff.

RNA quality analysis 

Users may arrange to have the quality of their RNA samples assessed on the Bioanalyzer. 

Data Analysis: 

Bioinformatics specialists are available to assist with data reduction and analysis.

Procedures performed by the user:

Preparation of RNA.  

The core facility staff does not extract and prepare RNA from cells or tissues.

Probe labeling and hybridization.  

For custom arrays, all hybridization is performed by the user.  The core facility will not perform hybridization of custom arrays.  Suggested protocols can be found at:       http://lgsun.grc.nia.nih.gov/cDNA/

 Fee Schedule for Custom cDNA microarrays (all prices are estimates and are subject to change): 

Mouse 15k gene set:

Complete set (15 membranes)                          $560/15 membranes

Standard subset (~1,152 genes/membrane)       $ 40/membrane

User-owned gene sets:

Use of MJ Research Tetrad                              $ 2.50 per 96-well plate

Spotting Charge                                                 $ 110 per 40 copies (1 run)

Membrane Charge                                             $ 45 per 40 copies (1 run)

RNA quality assessment                                $ 26.25 per complete assay