Gene expression service - frequently asked questions

What is gene expression analysis?

The use of Affymetrix GeneChips® allows for the simultaneous differential analysis of over 30,000 unique transcripts between distinct biological samples.  Gene expression analysis by microarray refers to the analytical process whereby nucleic acids from experimental samples are labeled and hybridized with small DNA fragments printed on quartz microarray chips, followed by imaging of the microarray, normalization and statistical analysis of the resulting data. An in-depth discussion of gene expression is provided in the technology overview section of the Affymetrix web site. 

What is the minimum number of samples that should be analyzed to identify differentially expressed genes?

To ensure confidence in the results, we recommend a minimum of three biological replicates per condition (i.e. genotype or treatment).

How do I initiate a gene expression analysis project?

Please direct inquiries to JAX® Services at jaxservices@jax.org.

Where do I ship the array chips?

For all Affymetrix GeneChip® experiments, arrays must be ordered directly from Affymetrix with your address in the "Bill to" line and The Jackson Laboratory address on the "Ship to" line on your PO. The chips must be drop shipped directly from Affymetrix to our facility.

Ship to address:
Gene Expression Service
c/o Sonya Kamdar
The Jackson Laboratory
RL-4; Room 3035
600 Main Street
Bar Harbor, ME 04609

On what chips can you offer services?

We offer gene expression analysis on mouse samples only.  We provide services for both the Affymetrix GeneChip® Mouse Gene 1.0 ST Array and Affymetrix GeneChip® Mouse Genome 430 2.0 Array. Please register your interest in the use of other chips with JAX® Services via email.

What is the difference between the 430 2.0 and 1.0 ST arrays?

The most significant difference between the two arrays is that the GeneChip® Mouse Gene 1.0 ST Array  contains on average 27 probes spread across the length of the transcript while the The GeneChip® Mouse Genome 430 2.0 Array has on average 11 probes located only at the 3’ end of the transcript. Other differences are the updated gene content of the 1.0 ST array and its reduced cost compared to the 430 2.0 array.

For more information on these arrays, please visit the Affymetrix website

How do I find out about the status of my project?

You may find out about the status of your project by contacting your Project Specialist by phone or email. The Jackson Laboratory will communicate your project status routinely at the following points:

  • Upon receipt of samples to the GES
  • Upon completion of the array scanning
  • Upon completion of the data analysis

If at any point in the study, QC markers are not met, the Product Specialist will contact you to review the issue and discuss your options.

Can I send samples for analysis directly to your facility?

No. The Jackson Laboratory is not providing gene expression analysis services on samples from external sources at this time.  Please do not send samples directly to The Jackson Laboratory. Please register your interest in our ability to provide this future capability with JAX® Services via email.

Can you perform analysis of the raw data?

Yes. We normalize the distribution of log transformed intensities across the arrays, apply the appropriate statistical test, and deliver ranked lists of differentially expressed genes. The R/maanova package is used to analyze groups of samples with most experimental designs. The raw permutation p-values are adjusted to address multiple testing using the R/qvalue package. Ranked results are annotated with the latest information.

A report will be generated including all methods, QC data, normalized intensities for all genes, and a list of statistically significant hits for differential expression.

Can you provide raw data?

Raw data is provided in the final report, described above.  We can also provide raw data that has not undergone extensive analysis, but has been checked using our standard QC procedures. Requests for raw data without additional analysis must be made at the time a project is quoted.

What protocols are used for Gene Chips®?

The following protocols are used for Gene Chips®:

How and when will I be invoiced?

All prices for Gene Expression Service projects are priced by quotation, based upon study design. A Purchase Order is required for project initiation. All projects will be invoiced at the time of data delivery. The quote will include information on pricing for additional consultation after delivery of the final report.