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Frequently Asked Questions
AFFYMETRIX GENECHIP RESOURCE FAQ
- What are the sample
requirements?
- Are the chips reusable?
- What is the turnaround time?
- What kind of data is provided?
- Do we get help in understanding data?
- What about the in depth data
analysis?
- Do we get our remaining, unused samples back?
- What is KARMA?
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Links to vendor support pages
1. What are the sample
requirements?
Very good quality RNA is extremely
important for the success of microarray experiments. RNA should be devoid of
genomic DNA. The RNA can be total cell RNA, as we do not believe that there is need
to isolate poly (A) RNA. A picture of the electrophoresis profile on native agarose gel (showing the loading wells) should be submitted along with the
samples.
Minimum of 7 μg of total RNA is required
for Affymetix microarray analysis. However we would prefer to have at least 20 μg so that we have enough material if experiment needs to be repeated in case of
any mishaps.
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A260/A280 should be
at least 1.8.
-
The RNA needs to be re-suspended in
DEPC-treat water between 1 to 3 μg/μl
concentration.
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The samples need to be hand delivered or
shipped on dry ice to Affymetrix Resource facility personnel.
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Each RNA sample must be properly labeled
as described in sample submission requirement form.
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The Affymetrix Resource service request
form must accompany all samples. The control or baseline sample must be clearly
mentioned on the service form.
2. Are the chips reusable?
No. Chips cannot be reused.
3. What is the turnaround time?
We expect to provide results within 3 to 4 weeks
after the samples are delivered to the facility. This may vary slightly from
time to time depending upon the number of samples queued and the proper
functioning of the instruments. When we receive your samples, we may give the
estimated turn around time. However, over 90% of the time, we deliver the
data within two weeks time.
4. What kind of data is provided?
All data generated using GeneChip Operating
Software
is provided to the user via the Yale Microarray Database (YMD) along with a user
name and password. Upon request, more in-depth data analysis using commercially
available software such as NetAffx will be provided at
additional cost.
5. Do we get help in understanding data?
Yes, help certainly will be provided to understand
the data. Similarly, if requested, training in usage of GeneChip Operating Software will also be provided. In order to accommodate these requests it is
necessary to schedule an appointment in advance and a service charge of $70.00/hour will be applicable to these services.
6. What about the
data analysis?
In-depth data analysis using commercially available
software (GeneSpring, Affymetrix data mining tools) service is provided by
Biostatistics Resource at
additional cost. Please contact
Aiping Lin at 203-737-1891
or
aiping.lin@yale.edu.
7. Do we get our remaining, unused samples back?
It is the responsibility of the investigators
to collect unused/or left over products (total RNA, cDNA, cRNA,
fragmented cRNA, hybridization mix). We will store them in the facility for a
period of 30 days after the completion of the project. After that period
samples will be discarded without any notice.
8. What is KARMA?
KARMA is cross-platform array comparison
interface which allows comparison of array content both within and across
species for all the arrays available through Affymetrix and the Microarray Resource
at Yale. The information about the genes present on any array also could be
obtained using this interface. KARMA is very flexible and data may be retrieved
based on many specific search criteria.
9. Links to vendor support pages
The following links have extensive online
support:
Affymetrix
Applied Biosystems
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