Colorado State University GeneChip Microarray Core Laboratory
The Affymetrix GeneChip Core Laboratory at Colorado State University is located within the Orthopaedic Research Center on South Campus. The core is a full service facility for investigators with interest in the many applications of genomic research.
Contact Information
Erin Duffy Petrilli
CSU GeneChip® Core Facility Technician
eduffy@lamar.colostate.edu
(970)297-4153
Dr. David Frisbie
Manager Orthopaedic Research Center
Director CSU GeneChip® Core Facility
dfrisbie@colostate.edu
Additional Resources
Statistical/Bioinformatics Analysis
Analysis is the responsibility of the investigator, however experienced help is available through CSU Statistics Dept
Contact Dr. Hari Iyer in Statistics for further information
Hari@stat.Colostate.edu
Collaborations are also welcome, for information please contact core personnel
Pricing Information
Pricing Breakdown
Price is based on Cost of Target Preparation, Array and Technician time. Please note that pricing and availability is dependent upon the vendor and is subject to change at the discretion of Affymetrix Technologies. This can not be controlled by CSU core.
Current Pricing
One Cycle Target Preparation
$170.44 per reaction (one sample per rxn)
Two Cycle Target Preparation
$209.16 per reaction (one sample per rxn)
Quality Control Using Agilent Bioanalyzer
Lab on a Chip RNA Pico Chip $24.13 per run (up to 11 samples per run)
Lab on a Chip RNA Nano Chip $20.86 per run (up to 12 samples per run)
Array Cost
Variable, see array pricing chart or call for quote
For Custom and DNA arrays please call core technician for Pricing and availability
Technician Hours
$29.00 per hour (no more than 50hrs per 12 samples)
Target Preparation One Cycle RNA(1-15µg)
Pricing for One Cycle Target Labeling Reaction based upon a 12 sample run:
Reagents and Kit: $170.44 per sample
Technician Cost: $108.75 per sample
Total processing cost per sample not including array or quality control: $279.19 per rxn
Target Preparation Two Cycle RNA (10-100ng)
Pricing for Two Cycle Target Labeling based upon a 12 sample run
Reagents and kit: $209.16 per sample
Technician Cost: $120.84 per sample
Total processing cost per sample not including array or quality control: $330.00
Quality Control Measures
QA/QC using Agilent Lab-on-a-Chip
Quality control during processing is optional, however Affymetrix, as well as the core facility highly recommend.
Cost based on running 12 samples
Nano Chips for large concentrations RNA
One chip (max. 12 samples) cost per chip $20.86
3 QA/QC Checks = $62.58
Pico Chips for small concentrations RNA
One chip (max 11 samples) cost per chip $24.13
3 QA/QC Checks = $72.39
Array Pricing
| GeneChip Array | Cost |
| Human Genome U133A | $369.00 |
| Human Genome U133A Plus 2.0 | $430.50 |
| Human Genome U133A 2.0 | $287.00 |
| Human Genome U133B | $369.00 |
| Human Genome U133 Set | $369.00 |
| Human Genome U95Av2 | $369.00 |
| Human Genome Focus | $205.00 |
| Rat Expression 230A | $348.50 |
| Rat Genome 230 2.0 | $410.00 |
| Rat Expression 230B | $348.50 |
| Rat Expression Set 230 | $348.50 |
| Rat Genome U34A | $348.50 |
| Rat Genome U34B | $348.50 |
| Rat Genome U34C | $348.50 |
| Rat Toxicology U34 | $205.00 |
| Rat Neurobiology U34 | $205.00 |
| Mouse Expression 430A | $369.00 |
| Mouse Genome 430 2.0 | $430.50 |
| Mouse Genome 430A 2.0 | $287.00 |
| Mouse Expression 430B | $369.00 |
| Mouse Expression Set 430 | $369.00 |
| Murine Genome U74Av2 | $369.00 |
| Murine Genome U74Bv2 |
$369.00 |
| Murine Genome U74Cv2 | $369.00 |
| Arabidopsis ATH1 Genome | $328.00 |
| Bovine Genome | $287.00 |
| Canine Genome | $287.00 |
| C. elegans Genome | $328.00 |
| Drosophila Genome 2.0 | $328.00 |
| Drosophila Genome | $287.00 |
| E. coli Genome 2.0 | $188.60 |
| E. coli Antisense Genome | $328.00 |
| P. aeruginosa Genome | $328.00 |
| Plasmodium/Anopheles Genome | $328.00 |
| Soy Genome | $430.50 |
| Test3 Arrays | $82.00 |
| Test3 Format 1 | $123.00 |
| Test3 Format 2 | $106.60 |
| Test3 Format 3 | $90.20 |
| V. vinifera Genome | $287.00 |
| Xenopus Genome | $328.00 |
| Yeast Genome 2.0 | $188.60 |
| Yeast Genome S98 | $328.00 |
| Made to Order Custom Arrays | |
| B. subtilis Genome | $328.00 |
| S. aureus Genome | $307.50 |
| Barley Genome | $328.00 |
| Human X3P | $430.50 |
Pricing and Availability of Chips and Reagents at the discretion of Affymetrix Technologies and is subject to change. Any changes will be updated and posted as soon as they are known by the core facility. For custom orders please contact the core.
Sample Processing and Technician Time
- Users have the option of preparing their own sample from RNA isolation to Hybridization, or submitting total RNA starting material and having the core technician complete the process from start to finish.
- Sample processing takes 4 days from drop off to data collection
- Cost of Technician processing based upon running 12 samples from start to finish is $108.75 per sample for One Cycle and $120.84 per sample for Two Cycle processing. This is cost of technician time only, reagents, kits, arrays and quality control measures are not included in this price.
- Individual quotes and pricing are available for proposals, grants and applications, please contact core personnel for information
Data Distribution
- Data and results will be delivered in electronic form on CD.
- All files generated during chip scan and GCOS analysis will be included in raw form.
- Files must be zipped during export from Affymetrix GCOS software, and therefore will need to be imported using Affymetrix Data Transfer Tool (DTT) which is available by download from the Affymetrix webpage.
- Hard copies or print outs are available by request.
- Copies of technical notes and QA/QC checks are automatically included along with the data CD
- Unfortunately, due to the size of the files created, it is not possible to send results via e-mail.
The Integrated GeneChip® System
The GeneChip Core Laboratory uses the latest Affymetrix technology and equipment including the GCOS 3000 scanner and Fluidics Station 450. Analysis assistance is available through the CSU statistics department and array software is widely available.
Product Applications
RNA Analysis
One Cycle Analysis of Total RNA
1-15µg starting material
Two Cycle Analysis of Total RNA
10-100ng starting material
mRNA
0.2-2µg starting material
Probe Selection
Experiments conducted by tiling all possible 25mers for >100 yeast genes on an array.
Developed probe selectiom algorithms to select probes that would linearly correspond to concentration of message based on a thermodynamic model.
Compared predicted and actual probe performance.
Compared detectiom call accuracy between probe sets with differing number of probe pairs.
Probe Selection Summary
Physical model accurately predicts probe hybridization intensity and slope.
Empirically determined from large training set of complex spike mixtures.
Latest algorithms select probe sets based on quality metrics, spacing, and cross-hybridization using optimization.
Product Applications
DNA Analysis
10K Mapping
Custom Arrays
SNPS
CustomSeq Benefits
Faster, more efficient and cost effective
Completed sequences 48 hours after you begin
Minimal alignment, curation, or hand-editing
Efficiency enables large novel experiments
More information in a single experiment
30 kb double stranded, both sequence and genotype
Custom content defined by the researcher
Only at the beginning of technology curve
Reliable and accurate
>99.99% accuracy with call rate >90%
>99.99% reproducibility
References
Affymetrix Technologies
Proprietary information was used as a courtesy of Affymetrix Technologies to create many of the graphics and images in this presentation.
More information can be found at their website: www.affymetrix.com
Special thanks also to our Field Applications Specialist Katrin Stapleton, PhD for her contributions to slides
CSU Orthopaedic Research Center Laboratory