Affymetrix Core Facility

Affymetrix GeneChip systems utilize proprietary technology, which exploits photolithographic fabrication techniques for light-directed chemical synthesis. The process results in extremely high-density arrays of specific oligonucleotide probe sets synthesized directly onto their glass substrate, which is then placed in a plastic cartridge for easy and safe hybridization, staining, washing, and handling. Affymetrix's software performs statistical algorithms of scanned images to analyze the expression data. Further information is available through the Affymetrix and NetAffx websites linked below. The Functional Genomics unit has the Affymetrix 3000 scanner and is capable of processing all Affymetrix GeneChips. Affymetrix Core Service Order Form is avaliable for sample submission. For a complete list of Affymetrix GeneChips available please see http://www.affymetrix.com/products/arrays/index.affx. In order to allow electronic transfer of results please open an ftp account by filling out and submitting an ftp request form to Keith Fraizier (frazier@illinois.edu)

For further information and services fees, contact: Carole Wilson or Mark Band in the Functional Genomics Lab at (217)244-3929.

RNA Sample Requirements for Eukaryotes and General Information for 3' Expression Arrays

OD260/OD280 ratio must be 2.0 (1.7 - 2.1 acceptable)
OD260/OD230 ratio must be > 1.0
Must submit 500 - 1000 nanograms total RNA (minimum concentration of 50ng/ul)
Picture of Total RNA Gel Electrophoresis submitted with service order form (download below) or alternatively
a Bioanalyzer assay.
P.I. supplies Probe Array Chip(s)

Core Performs

cDNA synthesis and clean-up
IVT with biotinylation and clean-up
- Quality and Quantity check of cRNA
cRNA fragmentation
1X Hybridization Cocktail
- 16 hour hybridization in Affymetrix GeneChip Oven 640
Stain/Wash chip in Affymetrix Fluidics Station 450
Scanning on Affymetrix GeneArray Scanner 3000
Initial Image and Data Analysis
Data will be transferred to a protected ftp site for client access.

RNA Sample Requirements for Eukaryotes and General Information for ST Expression Arrays

OD260/OD280 ratio must be between 1.7 and 2.1
OD260/OD230 ratio must be > 1.0
Submit 1000 nanograms total RNA (minimum concentration of 50 ng/ul)
Submit a photo of total RNA gel electrophoresis with service order form (download below), or
A Bioanalyzer assay
P.I. supplies probe array chips

Core Performs

Cycle 1 cDNA synthesis from polyA and non-polyA mRNA
IVT and clean-up
Quality and quantity check of cRNA
Cycle 2 sense strand cDNA synthesis incorporating dUTP
RNase H hydrolysis of cRNA template
cDNA clean-up
Quality and quantity check of cDNA
cDNA Fragmentation at dUTP residues
cDNA terminal biotin labeling
Hybridization cocktail preparation
16-hour hybridization in Affymetrix GeneChip model 645 oven
Stain/wash in Affymetrix model 450 fluidics station
Scan with Affymetrix GeneChip model 3000 scanner
Initial image and data quality control check
Transfer of data to a protected ftp site for client download

Affymetrix Core Facility

RNA Sample Requirements for Eukaryotes and General Information for 3' Expression Arrays

Core Performs

RNA Sample Requirements for Eukaryotes and General Information for ST Expression Arrays

Core Performs

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