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
  • New! Clariom D and S
  • Human Transcriptome 2.0
  • GeneChip 2.0 ST (1.0 as well)
  • Human PrimeView
  • 3’ Expression Analysis
MI-Ready Arrays

State of the art oligonucleotide deposition

Visit MI-Ready Page

Exonic Evidence-Based Oligonucleotide:
  • Human 48.5K and Mouse 38.5K
  • 70-mer oligonucleotides
  • Full coverage of Refseq transcripts with additional coverage of splice variants
Rat MI-Ready:
  • Oligonucleotides of 68 nt mean length
  • Designed by Operon Inc. in 2008
  • 34,717 transcript probes representing genes and exons from Ensembl release 37 for Rattus norvegicus
Extensive set of quality control features for robust data analysis
Custom Arrays

(contact us)
 
  • 1000 to 3000 features
  • Animals – cattle, nematode, dog, fruit fly, chicken, pig, and frog
  • Major crop, model plants, fungi, and bacteria


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). 
ORB utilizes the Web Gestalt algorithm to identify functional pathways where the differentially expressed gene sets are over represented.