The Genome Sequencing Center at Washington University has received funding from NHGRI and HHMI to produce
and distribute microarrays for use by C. elegans investigators. We feel that providing a common resource will enable comparability
of microarray data sets between C. elegans laboratories. The microarrays will contain long oligomers (nominally 60 mer) that are
designed to uniquely represent each gene in C. elegans (one oligo per gene), placed onto treated glass slides using split pin
technology. Also included on-array will be long oligomers representing unique E. coli genes, thus allowing investigators to assess
relative contamination of input C. elegans RNA samples with E. coli RNA. We also intend to spot up to 10 different long oligomers
that represent unique Arabidopsis thaliana genes. RNA samples that correspond to each A. thaliana element can be purchased
from Stratagene (www. Stratagene.com) by end-users, and added to their reverse transcription reactions during work-up of
C. elegans samples. This combination of A. thaliana oligo elements and RNAs will act as controls for cDNA and labeling reactions,
as well as providing a source of array data normalization that is independent of sample preparation.
The timeline for this project INCLUDED a pilot project that is NOW
COMPLETE, and HAS SOLIDIFIED our proposed approach at a trial level,
before proceeding to full genome arrays. In the pilot project, we have
designed oligos for ~300 C. elegans genes, using an in-house developed
algorithm that selects oligos unique to each gene with proximity to the
gene 3'end and with a minimum of secondary structure potential. The Tms of
all oligos were uniformly held to within +/- 3 °C, based on nearest
neighbor calculation. Oligos were synthesized by a commercial group,
according to our design specifications. The oligos were spotted, along
with the control oligo types mentioned above, and subjected to our planned
QC procedure. As a secondary QC, a few arrays were hybridized in-house,
using mixed-stage worm RNA to assess quality of hybridization, etc.,
according to our current protocols. Arrays also were distributed to two
test laboratories in the U.S. and WERE probed with previously
characterized RNA populations.
The whole genome arrays are now available to end users at a cost of $90 (US) per array,
with a limit of 10 arrays per PI laboratory per month. Please click the link at the left to
"Distribution and Purchasing Information" for details. We
welcome input toward making these arrays as highly useful as possible to
worm researchers. Please address comments to
elegans.array@watson.wustl.edu.
Sincerely,
Elaine R. Mardis, Ph.D.
John Spieth, Ph.D.
Washington University School of Medicine
Genome Sequencing Center
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