Penn Microarray Core Facility Fee Schedule

The modular fee description listed below reflects the Facility's goal to offer flexibility in services and pricing appropriate for many kinds of projects. Typical projects submitting total RNA for Affymetrix profiling should budget $425 per GeneChip and $450 per RNA sample to be processed. For example, preparation and labeling of four RNA samples costs around $1800 including labor, and if each is hybridized to an Affymetrix GeneChip (such as the human U133+v2.0 chip)the arrays would cost $1700. The budget for this project would therefore be $3500.

Labor charges are $70 per hour. Projects for clients not affiliated with the University of Pennsylvania, CHOP or Wistar will be assessed a 10% surcharge on all Facility fees. RNA extraction from tissue or cell samples will incur additional labor, as will double amplification of small samples.

Fee schedule

  • RNA isolation (1), per sample
    • Oligotex or RNeasy - $18.00
    • Tri-reagent - $27.50
  • Affymetrix target preparation (2), per sample
    • with Affy Test3 chip - $550.00
    • without test chip - $450.00
  • Affymetrix array hybridization and scan - $58.00 per GeneChip
  • Propagation of custom or commercial clone sets - $7.50 per 96-well plate
  • Clone set plasmid purification (3), per 96-well plate
    • Qiagen, Millipore or Invitrogen - $110.00 to $138.00
  • Clone set probe PCR for arraying, per 96-well plate
    • various grades of Taq and clean-up methods - $154.00 to $263.00
  • Clone set arraying, per 50 slides
    • various substrates and attachment chemistries - $605.00 to $850.00
  • Target preparation and hybridization to arrayed clone set (4), per sample
    • RNA amplification + labeling - $51.00
    • non-amplified target labeling - $22.00 for CyScribe, $49.00 for 3DNA dendrimer label
  • Lab work - $70.00 per hour
  • Training (general experimental design, protocols, data analysis) - $70.00 per hour
  • Consultation (facility resources, specific project updates and analyses) - no charge
  • Scanning Affymetrix or glass slide arrays not produced in Core Facility - $20.00 per scan


  1. Provide sufficient cells or tissue for 5 ug total RNA per assayed sample. Transcript profiling from less RNA is supported - please inquire.
  2. Affy Test3 chip provides quality control for sample labeling and hybridization, and can be used with RNA from several plant, animal, bacterial and yeast species.
  3. Recommended for uncharacterized libraries and clones, may be optional for previously sequenced targets.
  4. A number of fluorescent and metal microsphere labeling methods are available. Highest sensitivities may be achieved by combining protocols such as RNA amplification and resonance light scattering.

The Penn Microarray Facility operates on a cost recovery basis and all fees will reflect the actual expenses of reagents, consumable labware and service contracts, but do not incorporate charges for instrumentation purchases. Customized pricing will be available for non-standard protocols or method development in support of new projects.

When planning any project that will utilize services offered by the Penn Microarray Core Facility, please contact Don Baldwin to discuss experimental design, available resources and data analysis:

277 John Morgan Bldg.
Philadelphia, PA 19104-6082
dbaldwin {at}
215-898-3675 fax 898-4227

Last Updated on 7/15/04

Facility Description
Fee Schedule
Forms and Guidelines
Array Examples
Links of Interest

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