Cancer Genomics Core
Frequently Asked Questions
What must be done prior to bringing in samples?
First a Sample Submission form must be filled out and e-mailed to firstname.lastname@example.org or dropped off in Gray Building Room 3089. After a request is submitted, call Lou Craddock at 713-5103 or send e-mail to the above address to discuss when the samples can be processed. Once a Sample Submission Form has been completed and turned in, the investigator is committed to the process. The investigator will be held responsible for the purchase of any kits that were purchased to process his/her samples.
What happens if the quality of RNA is not adequate?
If the quality of the RNA is less than optimal you will be contacted and asked to make a decision about whether to proceed with the processing of the sample and/or batch of samples. If you decide not to continue processing or wish to provide a replacement a $10 charge will apply to defray the cost of the quality check. If you ask us to process a sample deemed questionable the facility cannot be responsible for poor yields in probe synthesis or poor data quality.
What happens if the stated concentration does not equal that measured by the facility?
The facility is aware that variations will occur when different people measure concentration. If there is a significant discrepancy, you will be contacted. If you desire to continue with the procedure and the facility is obligated to perform significant manipulations to the sample to achieve the necessary concentration, a small fee will be applied.
What happens if I do not have 15µg of starting material?
The facility is able to run samples with 10-15µg of total RNA and still expect good results. If you wish the facility to start processing samples with less then 10µg of cleaned RNA, we can take no responsibility for poor probe synthesis. All samples that are to be compared should be prepared using the same starting mass.
I plan to synthesize my own targets. Where can I get protocols?
The GeneChip Expression Analysis Manual is available directly from Affymetrix. This contains all the protocols for synthesis.
Do we get remaining samples and starting materials back?
The facility will store all starting materials, cleaned labeled cRNA, and hybridization cocktails for 30 days. All samples not picked up within that time will be discarded. If you think you might re-use any of the materials, remember to pick them. Chips will only be stored for the duration of the experiment; they are only usable for a single hybridization. Any leftover chips must be taken back to your lab. The facility is not responsible for any lost or damaged chips.
What happens if I get a defective chip purchased from the facility or Affymetrix?
If you purchased the chip through Affymetrix, the facility will notify you of the defect and how to proceed requesting a new chip. Replacements can take over a month to process.
Are chips reusable?
When can I expect my results?
Turnaround time can take anywhere from one to three weeks, depending on the size of the experiment and the current workload of the facility.
What type of data does the facility provide me with?
The core will extract data from each chip, and import into a MicroSoft XL spreadsheet.. The facility will provide copies of all the data files in addition to any comparisons requested on a CD.
Can I obtain help with my data?
Additional analysis and help with the data can be provided at an extra charge of $40 per hour for WFUMBC investigators