GeneChip™ Microarray Core


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Download the new Sample Submission Form for Microarray/QC. Download the 454 submission form for sequencing.  The core now requires users to fill out complete experimental and sample details.
Please make sure you have read the information on RNA extraction on the RNA submission page and have filled out the new appropriate online submission page. Failure to provide complete information will delay the processing of your chips.

RNA submission requirements: (3 extra ul are required to perform the QC)


Affymetrix Expression:

3' IVT Expression or gene 1.0 chips- Minimum starting amount 100-200 ng @ 30-100 ng/ul.

Standard Ovation- Minimum starting amount 25-100 ng @ 5-25 ng/ul. 

Whole Transcript Exon Chip- Minimum starting amount 1-2 ug @ 100-200 ng/ul.  

 

Nimblegen Expression:

1-plex, 4-plex, or 12-plex- Starting amount 10 ug @ 1-2ug/ul. 

DNA: 454 Sequencing: The procedure requires a minimum of 2 µg of double stranded DNA with a minimum concentration of 50ng/ul in TE Buffer. For LMW DNA, 70-800bp, 1microgram is required. The concentration should be verified by PicoGreen Fluorometry . Ideally, DNA starting material should be in pieces of >1.5Kb
SNP Assay: The Labelling Procedure requires 1µg of high quality genomic DNA with a minimum concentration of 100ng/ul.
Chromatin: A total of 4 µg of PCR amplified chromatin DNA in 8 µl volume (conc. of 500 ng/µl) may be submitted to perform ChIP-chip Hybridization Assays.
Samples should be submitted in person to the Core Laboratory along with the sample submission form, Monday through Friday from 10:00AM to 5:00 PM. It is best to schedule an appointment either by phone (858-552-8585-ext7100) or email (genechip@vapop.ucsd.edu) prior to submission of samples and chips. Samples may be placed in ice or dry ice (depending on distance traveled) and brought to the Core facility. All information on the sample submission form must be filled out. Samples and Chips will then be numbered and stored at the appropriate temperature until lab work begins.  Any remaining unused sample will be stored @ -80 degrees for up to two years.  After that time the sample maybe discarded. 
Chips: Chips may be bought from Affymetrix (1-888-DNA-CHIP) and shipped to the lab or directly to the Core.
Purchase Order Number: The sample submission form requires a Purchase Order Number (PO #) from the investigator’s institution for billing purposes.

1. Brazma et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data,  Nature Genetics, vol 29 (December 2001), pp 365 - 371.