Planning and Ordering Custom Arrays

Custom arrays are printed at Wistar's Genomics Core Facility for Investigators interested in examining genes that are not currently on our arrays, or smaller sets of genes that allow for more replicates per array. This page contains information about selecting genes, formatting array requests and the price. If there are other specific questions that you need answered, please contact arraysupport@wistar.org or Celia Chang @ 215-898-3902.

There are two models for creating the custom array:

• Model  #1) Investigator requesting array provides a list of genes needed on the array to the facility and our staff picks the clones, PCR amplifies cDNA inserts, analyzes PCR products, and arrays the sample. The investigator will be responsible for the costs but the core lab will take responsibility for amplifying and arraying chosen genes.  A clone picking charge plus the normal set-up charge will apply for all clones in our libraries mouse or human.
  In order to search our database of clones we currently have available please go to our FTP site. If we do not have your specific clone of interest the easiest way to find the gene is to search the Research Genetic's cMiner www.resgen.com/resources/apps/cminer/ or Clone Ranger www.resgen.com search tools available on their website or by using the search tools on  Incyte's website https://www.incyte.com/gxg/mainmenu.jspclone database.**Clones that are not in our library must be purchased by the investigator and supplied for use on the arrays.  
  
  
• Model #2) Investigator requesting array provides PCR products and/or purified plasmid DNA with concentrations to the facility. The concentrations of PCR products should be at least 0.08ug/uL, and 2-5ug/uL for plasmid DNA to ensure dependable spotting. PCR products are always preferable. **Only the set-up charge will apply in this instance.

All array requests must be submitted along with an excel spreadsheet indicating which clones are desired if we are to pick clones. If the investigator provides the DNA the excel spreadsheet should include all relevant annotation such as the accession or clone ID number, and current unigene cluster ID.

            All pricing for arrays is dependent on the number of array elements time required to amplify the clones of interest. Pricing for the clone picking is available on this price sheet. We will provide all of the housekeeping genes for Human or Mouse arrays from our pre-selected plates of PCR products.

            The printing is commonly done using the Affymetrix GMS-417 Arrayer on positively charged nylon. We may also use the larger Biorobotics TAS arrayer depending on the application and scheduling of your array.

**Note: For arrays with under 200 array elements we regularly print at least 42 slide sized arrays in a single run, depending on the viscosity of the solution, and the concentration of DNA in the sample..

**Radioactive arrays do not have an internal control and therefore must be normalized by dividing the intensity of each array element by the median intensity of all array elements. The underlying assumption for this scheme is that most genes' expression level does not change in a cell and therefore their signal intensity should remain similar on the array. Even if the labeling or washing efficiency differ between samples the bulk the large majority of all genes maintain the same signal ratios within an array.

If you use less than 50 genes on an array (for instance genes chosen based on high variance of expression between samples in larger arrays) it may be difficult to use our current normalization model with confidence. This is because all of theses genes' expression level may change significantly due to the experimental condition and change the denominator independently of labeling or washing conditions. It is therefore important to include House keeping genes and other genes that are expected to remain constant across experiments.

**Questions: Direct emails to arraysupport@wistar.org