NEW: JAX® Gene Expression Service Offered

JAX® NOTES Issue 509, Spring 2008

Need a quick, accurate, affordable way to analyze gene expression in one or several mouse tissues? Our new Gene Expression Service may be just what you're looking for. We have successfully performed this service thousands of times for our own scientists and are now offering it to the broader scientific community.

Among the many features of this service, two are particularly attractive:

1. It can be used to assess the gene expression profile for any tissue from our selection of over 3,500 JAX® Mice strains, saving you the trouble of having to obtain the mice, prepare samples, and assess gene expression yourself.

2. Our analysis technique is highly sophisticated and has more capabilities than other ones available (Wu et al. 2003; Cui et al. 2005).

Image from our JAX® Services website under service details. View a sample report on page 18 "Volcano plot for Diet 60 versus Diet 10 contrast with iterPLIER-processed data.

Service Details

Once you decide to work with us, your project is assigned to a Project Specialist, who schedules a phone conference with you and our scientists to establish an experimental design. The Specialist also keeps you informed about your project's progress. Typically, a project proceeds as follows:

  • We extract RNA, quantify it with the NanoDrop 100 spectrophotometer, and assess its quality with an Agilent 2100 Bioanalyzer;
  • We process and label the RNA according to array-specific Affymetrix protocols, using the Affymetrix platform, including both the Mouse 430 v2.0 GeneChip and the Mouse GeneChip®1.0 ST array. We assess quality control measures before hybridization, guaranteeing that arrays are not wasted on poor quality samples;
  • We hybridize labeled cRNA to the appropriate GeneChip®, wash the chip to remove non-specific signal, and scan it to generate the raw image data file;
  • We either deliver the raw data to you or analyze it ourselves;
  • We normalize the distribution of log-transformed intensities across the arrays, apply the appropriate statistical tests, and deliver ranked lists of differentially expressed genes;
  • We send you a report that includes all methods, quality control data, normalized intensities for all genes, and a list of statistically significant hits for differential expression.

Still have questions? Want to get started? Contact JAX® Services at jaxservices@jax.org, 1-800-422-6423, or 1-207-288-5845.

References

(Author in bold is a Jackson Laboratory Professor)

Cui X, Hwang JTG, Qiu J, Blades NJ, Churchill GA. 2005. Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 6:59-75.

Wu H, Kerr K, Churchill GA. 2003. MAANOVA: A software package for the analysis of spotted cDNA microarray experiments. Springer, NY. 49pp.

Yang H, Churchill G. 2007. Estimating p-values in small microarray experiments. Bioinformatics 23:38-43.