Genomics Array Services
DNA Array Analysis
The RTSF has a GeneChip Instrument System for the preparation, hybridization and fluorescent quantitation of Affymetrix GeneChips. The instrumentation and initial analysis are managed by GeneChip® Operating Software. For gene expression analyses, the investigator generates biotinylated cRNA, and these RNA samples are loaded onto appropriate test and genome chips, hybridized, washed, and stained under appropriate conditions. The chips are scanned and the resultant intensities analyzed for levels of transcripts of interest. GeneChip arrays are available for many organisms including Arabidopsis, C. Elegans, Canine, Drosophila, E. coli, Human, Mouse, P. aeruginosa, Rat, Xenopus, Yeast, and Zebrafish genomes.
Affymetrix® Submission
Prepare and quantitate cRNA using protocols in the Affymetrix Technical Manual. Provide 5 ug cRNA (adjusted concentration) for Test3 chips and 15 ug cRNA (adjusted concentration) for genome chips. Provide cRNA for fragmentation at RTSF in a final volume of 32 ul (correct volume with RNAse-free water). If both Test3 and genome chips are to be hybridized with one cRNA sample, provide 20 ug in a total of 32 ul for fragmentation. Internal controls will be added by RTSF prior to hybridization.
Generally, data from samples submitted by 3 PM (Monday-Thursday) will be available by 5 PM the following day. Data from samples submitted on Friday will be available by 5 PM the following Tuesday.
Pricing
| Service | Price/ Sample |
|---|---|
| Affymetrix – Transcript labeling (per chip) | $400.00 |
| Affymetrix – Scanning- Hybrid | $315.00 |
Agilent Array Analysis
RTSF offers processing and analysis services for the full line of Agilent microarrays. Agilent Technologies products include array platforms for analysis of gene expression, ChIP-on-chip, microRNAs, Oligo aCGH, and DNA methylation for a number of organisms, as well as generation of custom arrays in a number of formats. These include 1×244K, 2×105K, 4×44K, and 8×15K which allow 1, 2, 4, or 8 experiments to be conducted on a single slide respectively.
Scanning is performed on Agilents G2505B Array Scanner followed by data and QC analysis with their Feature Extraction software. The GeneSpring software package is also available for downstream analysis.
The pricing structure varies depending on the format of the slide. All prices below include labeling, hybridization, and scanning using Agilent kits and reagents. For pricing on arrays please inquire with RTSF or Agilent.
Pricing
| Sample Prep | Price/ Slide |
|---|---|
| 1×244K (one color) | $300.00 |
| 1×244K (two color) | $405.00 |
| 2×105K (one color) | $445.00 |
| 2×105K (two color) | $655.00 |
| 4×44K (one color) | $735.00 |
| 4×44K (two color) | $1155.00 |
| 8×15K (one color) | $1230.00 |
| 8×15K (two color) | $2075.00 |
| Agilent Scanning (customer use) | $12.00 |
Custom Spotted Arrays
The RTSF offers a custom microarray printing service. PCR products or oligonucleotides supplied by the investigator are arrayed on glass slides using a Genomic Solutions OminGrid robot with TeleChem Chipmaker pins (48 pin maximum capacity). Oligonucleotide design and synthesis services are available as well as assistance in preparing DNA samples for printing. For scanning and quantitation of fluorescent intensities both an Affymetrix 428 Array Scanner and an Agilent G2505B Scanner are available for use. A full service sample processing service and/or training is available for sample labeling, hybridization, and scanning (please inquire for pricing).
Pricing
| Service | Price/Slide |
|---|---|
Printing |
$4.90 - |
| Slide Scanning | $10.50 |
Microarray
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Illumina Bead Express
The BeadXpress Reader is a high-throughput, dual-color laser detection system that enables scanning of a broad range of multiplexed assays developed using the VeraCode digital microbead technology.
This platform supports DNA-, RNA-, and protein-based assays with the broadest multiplexing range in the industry. The VeraCode technology utilized by this system allows from 1 to 384-plex assays per well in a standard 96-well format.
Currently Illumina offers full design and synthesis services for either 96- or 384-plex SNP assays. SNP lists are submitted to Illumina’s Golden Gate Design Tool which will evaluate the suitability of each sequence. Once a list of acceptable SNP’s has been generated, it is submitted for synthesis. Both the 96- and 384-plex kits include enough reagents to assay 480 samples at a final cost of 22 and 12 cents per SNP respectively.
Pricing
| Service | Price |
|---|---|
| GoldenGate Genotyping Kit for Veracode, 48-plex | $5,040 |
| GoldenGate Genotyping Kit for Veracode, 96-plex | $5,990 |
| GoldenGate Genotyping Kit for Veracode, 144-plex | $8,294 |
| GoldenGate Genotyping Kit for Veracode, 192-plex | $11,059 |
| GoldenGate Genotyping Kit for Veracode, 384-plex | $18,432 |
| Processing Fee (per 96 well plate) | $800.00 |
