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Microarray FAQs
What should I do to start an experiment?
You should first contact
us via e-mail and be sure to provide your phone number. This allows
us to get back to you as quickly as possible to discuss the specifics
of your experiment, give you a quote, and establish time lines. Once you
have agreed to your quote and a purchase order number has been assigned
to your experiment, arrangements will be made for you to send your samples
to our facility on dry ice. All samples should be accompanied by a completed
sample submission form and a picture of an agarose gel or bioanalyzer
report of your samples.
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What type of arrays
can the Genomics Core Facility process?
We can prepare and process all Affymetrix GeneChip® arrays
(both eukaryotic and prokaryotic samples). We generally use standardized
Affymetrix protocols. However, if you need special services or protocols,
please discuss this with us.
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What type of starting
material does the Genomics Core Facility accept?
This depends on the type of Affymetrix array you plan to use in your experiment.
In general, we accept user-isolated total RNA, mRNA, genomic DNA, and/or
fragmented samples for the partial services.
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Does the Genomics
Core Facility isolate RNA and DNA from tissue or cells?
Yes, although a separate per-sample fee will be applied to extract these
starting materials.
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What happens if my RNA quality is not optimal?
All samples submitted will be analyzed on the Agilent
Bioanalyzer. If the quality of your RNA is less than optimal, we will
contact you and ask you to make a decision regarding the processing of
your samples. If you ask us to process a sample that we consider to be
of poor quality, we are not responsible if poor yields are obtained, leading
to unsuccessful hybridization and scan results. A second sample preparation
and hybridization will NOT be done free of charge. Please contact
us if you would like more information about the types of quality metrics
we perform.
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What if the submitted
samples do not meet the concentration requirement?
We understand that slight variations in concentrations occur when different
people measure concentrations. Unless the difference between the concentrations
you submit and the ones we measure are significant, we will continue with
the processing. If the discrepancy is significant, you will be contacted.
Please see our “Quantity” sections about providing additional
starting material. If we have to manipulate the sample in order to attain
the required concentrations, a per-sample surcharge will be applied.
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What does the Genomics
Core Facility suggest as a minimum amount of starting material to submit
for the full service?
Please review our “Quantity” and “Quality” sections
about minimum amounts of starting material. If you need further clarification,
feel free to contact
us.
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What amount of fragmented
material should I submit for the partial service?
Since the answer to this question is array-dependent, we suggest that you contact us regarding the particular array type you would like to use for your experiments.
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Should I choose the
full or partial service?
This usually depends on your needs and budget. However, allowing the core
to perform the full service reduces technical variation and leads to the
best results.
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Do I need to run a test3 array?
The test3 array from Affymetrix has hybridization controls from various
species. We recommend using the test3 array especially if you have never
done a study with us. The test3 array is priced less than the standard
arrays and allows us to make sure the hybridization protocol is optimal
for your sample. It is less expensive to modify a protocol for a failed
test3 array experiment than to have a failed genome array experiment.
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What is my turn-around
time?
Samples are handled in the order they are received. Once we start your
experiment, we will usually have results in less than one business week.
You can usually expect to receive a DVD copy in less than two business
weeks.
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What does the Genomics
Core Facility do with leftover DNA, RNA, hybridization cocktails, and
GeneChips?
We store all leftover DNA, RNA, and hybridization cocktails at -80°C
for one month from the finishing date of your experiment. Your GeneChip
arrays will also be stored at 4°C for one month from the finishing
date of your experiment. Please let us know if you desire to collect your
leftover DNA, RNA, hybridization cocktails, and/or GeneChips before the
one-month deadline. Please note that we will discard your sample materials
once the deadline has passed. You will receive notification when your
one month deadline approaches.
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What format of data
will I receive?
We will extract data from individual chips for you. We will give you the
.EXP (general experimental information), .DAT (.jpg image), .CEL (averaged
cell intensity), and the .CHP (data in Affymetrix software format) files
for each sample of your experiment. A .RPT (report) file containing all
the signal data can be produced using Affymetrix GeneChip Operating Software
(GCOS) or some other second- or third-party software.
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Can I get additional analysis of my data?
The Genomics Core Facility has a statistician and computers with software
licenses for GCOS and Data Mining Tool software (e.g. GeneSpring®,
SpotFire®, and Partek®). If you want further
analysis of your data, please contact
us for a cost estimate.
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I think my chip
was defective. How can I be sure and what do I do?
Defective chips are replaced free of charge by Affymetrix. We will contact
you if we suspect that your chip is defective. Affymetrix will request
a copy of the .DAT and .EXP files for a defective chip and on confirmation,
replace the defective chip. Please note that it usually takes a month
for the replacement.
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Can I buy chips
from the Genomics Core Facility?
We can buy chips for you from Affymetrix at prices significantly cheaper
than list prices. You may also buy the chips yourself and provide them
to us prior to the study. Please note that if you provide us the chips,
you are responsible for obtaining the replacements for any defective chips.
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Can I sell any leftover
chips back to Affymetrix or the Genomics Core Facility?
No. Unfortunately, chips are sold in packs of 2, 5, 6, or 30 which leads
to leftover chips if you do not have enough samples. We realize that chips
are expensive and budgets are tight. We suggest teaming up with another
lab to use up all the chips.
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