SUNYMAC FAQ

1. Where and how do I drop off my samples?

All samples must be brought to the Core Facility (WHA 3285) Contact Karen Gentile (315-464-3206) at least three days in advance to schedule a drop-off time.

Labs outside of SUNY Upstate, please contact Karen to discuss sample shipping.

Tissue:

  • Tissue samples that have been stored in RNALater can be brought up on wet ice.
  • Frozen tissue must be transported on dry ice.
  • Contact the Core Facility if you will be dissecting fresh tissue that will be processed immediately.

Cell culture:

  • Spin down cells and remove all media, then freeze the pellet immediately. Bring cells to WHA 3285 on dry ice.

Laser microdissection:

Contact Karen Gentile to schedule time on the LMD microscope. Total RNA can be extracted immediately after laser dissection. Alternatively, LMD samples can be frozen on dry ice and stored at –80C for processing at a later time.

Total RNA:

If you have extracted total RNA, you will need to bring it to the core facility on dry ice. If you have gel pictures or have measured your RNA concentration, bring those data to the lab with your samples. However, the Core Facility will quantify and check the quality of your total RNA sample with the Agilent Bioanalyzer at no additional charge.

Suggestions for total RNA preparation:

We suggest using the RNeasy mini-kit from Qiagen for total RNA extraction, although any method that results in high quality RNA is acceptable. Total RNA preparations should be resuspended in RNase-free water.

DNA:

  • DNA samples should be kept refrigerated, multiple freeze/thaw cycles can cause reduced call rates on the Human Mapping Arrays.
  • DNA should be shipped on blue ice or at ambient temperature.

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2. How much total RNA will I need and in what concentration?

Optimally, 8 micrograms of total RNA is suggested as starting material for the labeling process using the Affymetrix Standard One Cycle Protocol. However, we are able to label RNA starting from much smaller quantities (from small tissue biopsies or laser microdissected samples, for example), as long as the RNA quality is good using the Nugen kit. Total RNA samples can be dropped off at any volume and any concentration; we will adjust the volume at the Core Facility. Samples should be resuspended in RNase-free water.

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3. How should genomic DNA be prepared?

Genomic DNA for the Human Mapping Arrays is required to be of very high quality. Multiple freeze/thaw cycles and pipetting will cause genomic DNA quality to decline and may cause lower call rates on the Mapping Arrays.

Genomic DNA can be resuspended in either nuclease-free water or low EDTA buffer (10mM Tris-HCl, pH 8.0, 0.1mM EDTA, pH 8.0) This buffer can be purchased from Teknova (Cat.No. T0223). External link

We require 500ng of genomic DNA for each chip, at least 10ul at 50ng/ul. 

If your DNA is already prepared but resuspended in standard TE buffer, you must precipitate the DNA (we recommend Novagen PelletPaint External link) and resuspend in either water or the low EDTA buffer.

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4. How long after I drop off my sample will I have data?

The exact timing for completion of your experiments will depend on the number of samples you have and the total number of experiments being processed in the Core Facility at the time, but usually you will have your data within two weeks of sample drop-off.

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5. How do I get my data and what do I do with it?

When your samples are processed, you will be contacted by Karen. You can access your data in two ways:

  1. See Data Analysis Resources page for information about software programs that you can obtain from the Core Facility, or:
  2. CD/Memory Stick– Bring a CD or Memory Stick to the lab and we will copy your data files.
  3. For larger filed we will post your data for secure FTP download

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6. Is there a system for data storage at the Core Facility?

The Core Facility keeps all files associated with each experiment on a back-up drive in WHA3285. These files will be available at your request.

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7. What happens to my sample material?

The Core Facility will not store tissue samples or slides. Total RNA, cDNA, and hybridization cocktails will be stored at the Core Facility after your samples are processed, but we strongly encourage you to take all samples back to your lab for storage. A list of samples, concentrations, and approximate volume will be provided when you pick up your tubes.

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8. How much does it cost?

Contact Karen (315-464-3206, gentilek@upstate.edu) for current pricing.

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9. How do I pay for Microarray Services?

After your samples are processed and you have your data, your lab will be sent an invoice with your charges and instructions for payment.

If you are at SUNY Upstate, you can bring a signed Research Foundation Purchase Requisition with your grant account number to Karen. She will send you a copy of the completed form.

Labs outside of Upstate (including other SUNY schools) must pay by check, we are unable to accept PO numbers. Checks should be made payable to The Research Foundation of SUNY, with SUNY Microarray Core Facility referenced in the memo line. Send checks to:

Karen Gentile
Upstate Medical University
Neuroscience/WHA 3285
750 East Adams Street
Syracuse, NY 13210

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10. I have more questions– who do I call?

Call or email the Scientific Director Dr. Frank Middleton for questions regarding experimental design or data analysis and interpretation. Call or email the Technical and Administrative Director of the Core, Karen Gentile, for inquiries about sample preparation, processing, or billing and ordering:

Karen Gentile
315-464-3206
gentilek@upstate.edu

Frank Middleton
315-464-7721
middletf@upstate.edu

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Contact Us

For questions or to drop off samples contact:

Contact: Karen Gentile, Technical and Administrative Director of the Core
Location: Upstate Medical University, Neuroscience
Weiskotten Hall 3285
750 East Adams Street, Syracuse, NY 13210
Phone: 315 464-3206
Email: gentilek@upstate.edu