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Molecular Profiling
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To begin a transcript profiling project, purchase arrays or schedule service:
  1. Schedule a consultation with Tapan Ganguly gangulyt@pennmedicine.upenn.edu
  2. The principal investigator to be billed can create and manage projects by visiting How to request services Remember to authorize any users for your project who will be allowed to request service in step 3.
  3. Complete the appropriate service request form in the Service section and submit it online, entering the assigned Project ID. You will receive a confirmation email. To request work by the Facility staff on your samples, use the Request To Submit Samples link. To purchase catalog microarrays, reagents, instrument time and supplies, or custom printed microarrays for your self-service projects, use the Other Requests link. To reserve self-service instruments, use the Schedule Self-serve Equipment link.

Procedure for submitting RNA:

  1. Paper copies of the submission form are not accepted. Your online form will be reviewed, and returned if incomplete or unclear. The date and time we approve your electronic form will determine your priority in the sample processing schedule. Online forms are available from the Request to Submit Samples link in the Service menu.
  2. After the work request is approved, please take samples to 68 John Morgan Bldg. between 9am-4pm weekdays. Or, use the shipping address listed below. Samples without an electronic form, or forms without samples, will prevent the project from being scheduled until both are received.
  3. Sample sizes (provide at least 3ul extra for quality control):
    • If you provide 1 microgram or less of total RNA the volume should not exceed 10 microliters. The minimum mass is 0.5 nanograms.
    • Samples over 1 microgram should be at least 0.3 ug/ul. We can concentrate your samples by partial evaporation as long as the RNA is supplied in water.
    • If you are submitting previously amplified/labeled samples for Affymetrix GeneChip hybridization, provide at least 10ug biotinylated, fragmented cRNA at 0.5ug/ul if you used IVT linear amplification. From NuGEN ribo-SPIA amplification, provide the cDNA mass indicated in the NuGEN user manual.
    • microRNA projects should provide at least 250 nanograms of total RNA per sample to be labeled. Total RNA must be prepared using a method that preserves the miRNA fraction, such as Ambion miRVana or Qiagen miRNeasy. Enrichment of the miRNA is not necessary.
  4. Transport your samples on dry ice in a disposable insulated container to be left in 68 John Morgan; follow posted instructions for logging in your samples. Submit samples in RNase-free 1.5ml microtubes. Label every tube clearly, using exactly the same sample ID as on your submission form. Label the insulated container with your project ID.

RNA Guidelines:

Gel pictures of your samples are not required. Total RNA samples should have an A260/280 ratio of 1.7-2.1. The Facility will perform sample quantitation and quality control checks using the Agilent Bioanalyzer and Nanodrop spectrophotometer, which are effective even for projects using very small amounts of RNA. Most commercial RNA isolation kits provide adequate purity for transcript profiling; some Trizol extracts may benefit from additional column clean-up. DNase treatment is recommended for all samples and required for samples of less than 10ng RNA; this can be done on-column during RNA purification. Elute or resuspend your RNA in RNase-free water, and consider adding an RNase inhibitor such as Ambion's Superase-In. RNA in water can be concentrated by EtOH precipitation, or simply allow some of the volume to evaporate at room temp or in a SpeedVac. Do not allow RNA to dry completely, it will be difficult to redissolve.

Procedure for submitting tissue or cells:

  1. Paper copies of the submission form are not accepted. Your online form will be reviewed, and returned if incomplete or unclear. The date and time we approve your electronic form will determine your priority in the sample processing schedule. Online forms are available from the Request to Submit Samples link in the Service menu.
  2. After the work request is approved, please take samples to 68 John Morgan Bldg. between 9am-4pm weekdays. Samples without an electronic form, or forms without samples, will prevent the project from being scheduled until both are received.
  3. Provide enough material to extract at least the amounts of RNA listed in the Procedure for RNA described above. If your sample is from a cell culture, dump the liquid media, flash freeze the collected cells, and store at -80C before delivering on dry ice. Tissue samples should be securely wrapped in aluminum foil or a sealed tube, labeled with permanent marker, and flash frozen in liquid nitrogen. Store at -80C and deliver on dry ice. Samples saturated with RNALater should be pelleted and the RNALater removed before flash freezing and submission. Tissue samples may also be collected in Trizol and stored at -20C; use Trizol LS for liquid samples including cell sorting fractions.
  4. Transport your samples on dry ice in a disposable insulated container to be left in 68 John Morgan; follow posted instructions for logging in your samples. Submit samples in RNase-free 1.5ml microtubes. Label every tube clearly, using exactly the same sample ID as on your submission form. Label the insulated container with your project ID.
Human tissues or fluids will not be processed by the Facility. Please submit purified RNA.

Our overnight shipping address is:
Kathakali Addya
Penn Microarray Facility
68 John Morgan Bldg
3620 Hamilton Walk
Philadelphia, PA 19104-6100
telephone 215-898-3675

Ship samples on plenty of dry ice, and label both exterior and interior of package with your project ID.

Transcript profiling data will be provided as raw scanner images, processed images with quantitation, and/or data spreadsheets as appropriate. Quality control reports are also provided. The Facility works closely with the Penn Bioinformatics Core, and new clients are strongly encouraged to schedule a bioinformatics consultation to cover experimental design, analysis strategies and tools.

Facility business hours are 9am - 5pm, Monday to Friday

Quantitative PCR and Molecular Diagnostics

General Information
Before initiation of a study requiring collection of human or animal specimens, and testing by the Molecular Diagnosis and Genotyping Facility, for specimen collection, storage, and delivery to the Molecular Diagnosis and Genotyping Facility. Every study will use a study specific requsition form .

Contact Tapan Ganguly or Kathakali Addya to discuss project, specimen types, assay design, costs

  • Identify/provide journal articles on methods and controls
  • Request service online
  • Data returned to investigator via fax or email
  • Assistance with interpretation of results
Safety

All human and animal specimens must be treated as potential infection risks. Care should be taken to avoid over-filling of blood tubes, which is likely to be associated with leakage of blood and contamination of the external surface of the container. Needles must be disposed of with care into a "sharps" container. Syringes, swabs, or any other blood-contaminated materials must be placed in an appropriate contaminated waste container immediately after use.

Evacuated collection systems are now frequently used for blood collection, as there is less chance of blood spillage and thus exposure to blood-borne diseases.