From mutant umich.edu Wed Aug 22 09:52:21 2012
From: "Thompson, Robert" <mutantumich.edu>
Subject: RE: What gene arrays recommended to use for sheep?
To: Multiple Recipients of <sheepmodelsanimalgenome.org>
Date: Wed, 22 Aug 2012 09:52:21 -0500
I have "looked at" the Agilent Ovine array. In my analysis of the
annotations linked to this array, Agilent provides annotations for a VERY
limited number of probes. Hence, despite having many probes, interpretation
of results is extremely limited due to ineffective probe annotations. If I
recall (and I performed this analysis about one year ago), Agilent provided
annotations for about 2,000 of the 24,000 probes on this array (yes, that's
not a typo; two thousand out of twenty four thousand).
I have also used the Affy Bovine arrays. In my use of these, array data
variability limited the overall usefulness of the resulting gene expression
data. We also experienced limited success validating any array results using
qPCR methods. However, the probe annotation on this product is quite good
(at least for bovine).
Finally, we have used the newer Affy Ovine Gene_ST array. While the
annotation of this array is better than Agilent's Ovine array, the annotation
of this product is also weak. In our studies, we identified many probe sets
that were differentially expressed due to treatment but over two thirds of
these probes sets had NO ANNOTATION linked to them. I have asked Affy
repeatedly for the target sequenced used for their probe designs (a sequence
that would be useful in sequence comparisons across species (e.g. bovine)) but
they have thus far failed to provide this target sequence. I was told a
couple of weeks ago that this target sequence was available on the Affy web
site but I've looked and cannot find it.
I would love to hear from others who may have had better experiences.
Bob Thompson
University of Michigan
-----Original Message-----
.From: Gudrun Philomena Fiona Debes [mailto:gdebesvet.upenn.edu]
.Sent: Wednesday, August 22, 2012 9:53 AM
.To: Multiple Recipients of <SheepModelsanimalgenome.org>
.Subject: What gene arrays recommended to use for sheep?
Dear Sheep Research Community,
I would like to perform gene expression profiling with sorted sheep
lymphocyte subsets. What is your experience with [commercially] available
gene arrays? Many people publish arrays done with Affimetrix bovine arrays.
Is that useful? Has anybody used the Agilent ovine array? Maybe somebody
would be able to help me with a customized array?
Thanks for your advice,
Gudrun
--
Gudrun Debes, DVM
Assistant Professor
Department of Pathobiology
School of Veterinary Medicine
University of Pennsylvania
Hill Pavilion, Room 317
380 South University Avenue
Philadelphia, PA 19104-4539
Phone: +1-215-573-9167 (office)
+1-215-573-4713 (lab)
Fax: +1-215-746-2295
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