Gene Expression Microarray
Ocean Ridge Biosciences is a well-established service provider for Gene Expression Analysis utilizing microarrays from major manufacturer's including Affymetrix and Microarrays, Inc. ORB also provides follow-up validation of microarray results using real-time quantitative qPCR assays, as well as comprehensive data and gene set enrichment analysis services.
Our mission is to provide competitively-priced microarray results which are reproducible, sensitive, and accurate. In addition, we are committed to excellent customer service, full documentation of every phase of the project, and timeliness. Turn-around is 15 days or less for most projects. As part of our standard service we provide initial consultation on experimental design, and quality control reporting at multiple project phases. We offer modular analysis packages that ensure you pay for only the data analysis you require. At the same time we provide custom analysis (e.g. mRNA-microRNA expression correlation analysis) at very affordable prices. Follow-up support includes preparation of images for posters and grants, customized text for your methods section, and training on the use of pathway analysis software.
Description of Services
ORB provides complete processing services for microarrays produced by multiple vendors according to the manufacturer's recommended protocols. Choose from any of the available microarrays listed in Table I. Detailed descriptions are available by clicking on the array type. A comparison of various gene expression microarray platforms can be located in Table II.
Table I. Available Microarray Platforms
| Array Type | Technology | Highlights |
|---|---|---|
| Affymetrix | Visit Affymetrix Page |
|
| MI-Ready Arrays |
State of the art oligonucleotide deposition |
Exonic Evidence-Based Oligonucleotide:
|
| Custom Arrays (contact us) |
|
Table II. Comparison of Available Gene Expression Microarray Platforms
| Microarray | Total Probes1 | Probe Length2 | Probes per Set3 | Advantages | ||
|---|---|---|---|---|---|---|
| Human | Mouse | Rat | ||||
| Affy Clariom D | 6,765 | 6,022 | 5,946 | 25 | NA | Deepest transcriptome-level expression profiling, including interrogation of alternative splicing events and long noncoding RNA. Confidently detect rare and low-expressing transcripts, exons, and alternative splicing events that give rise to coding and long non-coding RNA isoforms(5-15 probes per exon, 4 per junction) |
| Affy Clariom S | 206 | 221 | 229 | 25 | 10 | Based on the best performing Clairom D probes to provide the most constitutive probes sets across known isoforms of a gene. Most intricate transcriptome-wide gene- and exon-level expression profiles, including the ability to detect alternative splicing events of coding and long non-coding RNA, in a single experiment |
| Affy Human Transcriptome 2.0 |
6,000 | NA | NA | 25 | 10 | Dense coverage at exon-level probes designed to measure all known transcript isoforms produced by a gene. Over 20K probes targeting non-protein coding content. (10 probes per exon, 4 per junction) |
| Affy 3’ Expression | 1,188 | 990 | 682 | 25 | 22 | Industry standard, most widely-published microarray; proven performance for gene-level analysis for well-characterized genes. Multi-species coverage available. |
| Affy Gene 2.0 ST | 1,350 | 698 | 610 | 25 | 21 | Exon-level coverage of whole transcriptome, reduced cost relative to 3’ arrays. Multi-species coverage available. |
| Affy PrimeView | 493 | NA | NA | 25 | 9-11 | Complete but focused coverage of the annotated human genome. |
| MI-Ready Arrays | 49 | 38 | 35 | 70 | NA | Superior cost and sensitivity for human, mouse, and rat. |
1, All counts are rounded to the nearest thousand and provided in thousands. 2, Probe length is given in nucleotides. 3, Probes per set are provided in each case for Affymetrix arrays, except the Clariom D array where probes are not segregated into distinct sets. The MI-Ready product designs also do not utilize probe sets.
The Standard Processing Service Includes:
• Spectrophotometric & electrophoretic analysis of RNA samples, with the option to replace samples at no additional cost.
• Amplification and labeling of cRNA and cDNA and QC testing of the amplified product.
• Hybridization, feature extraction, and basic data processing.
• A quality control report including multiple measures of signal-to-noise and reproducibility for each microarray hybridized.
The entire service is just $370 per sample for one-color hybridization*. To determine entire project price just add the cost of your selected microarrays and data analysis modules. See our Price List for complete pricing information. Don't forget to Contact Us to find out about current specials and discounts!
*Minimum 12 samples, see price sheet for other quantities.
Data Analysis Modules
- Standard Data Analysis:
Normalization, fold-change calculations, analysis of variance (ANOVA), hierarchical clustering, principal component analysis. - Gene Set Enrichment Analysis:
Examine over-representation of differentially expressed genes based on up to 4 fold-change criteria. - Custom Data Analysis:
MicroRNA-mRNA anti-correlation analysis, exon-level analysis, and more (please inquire).
