GEAW Quality Control and Image Analysis Challenge Data Set
Data
generated by Incyte Genomics for the purpose of assess quality
assurance parameters within micorarray experiments.
The dataset consists of
independent evaluations with 70 arrays from each of two different
manufactured lots. The hybridizations utilized three rna samples, one
from human placenta, one from human brain and the other from human heart.
Ten arrays in each set consisted of homotypic hybridizations; ie
placenta: placenta, brain:brain and heart:heart. The remaining 40 arrays
in each set consisted of differential experimental conditions. Ten arrays
each were brain:placenta, placenta:brain, heart:placenta and
placenta:heart, where the tissue listed before the colon was labeled
with Cy3 and that after the colon was labeled with Cy5. Incyte
UniGEM 1.03 cDNA microarrays consisting of approximately 10,000 PCR
products were utilized. An Axon scanner was used with GenePix image
acquisition software. The image analysis algorithm in GEMTools software
was used to quantify signal and background intensity for each spot on the
array. The Axon scanner was calibrated using a primary standard and a
secondary standard to account for the differences in scanner performance.
For the primary standard, hundreds of probe samples were prepared which
were fluorescently balanced in Cy3 and Cy5 channels as determined by a
fluorescence spectrophotometer. These probes were hybridized to
microarrays and the scanner PMT voltages were adjusted to give balanced
fluorescence and the greatest dynamic range. Using these PMT values, a
fluorescent plastic slide was scanned to obtain corresponding
fluorescent values. This secondary standard was used to calibrate other
scanners on a daily basis.
The arrays contained a set of spots consisting of PCR products derived
from 10 non-coding regions of Saccharomyces cerevisiae. These spots were
printed in quadruplicate at different points on the arrays. In vitro
transcripts of the yeast fragments were included in every labeling
reaction at predetermined Cy3:Cy5 input levels (fragment 22 at 123
pg:4pg, fragment 6 at 123pg:123pg, fragment 25 at 4pg:123pg, etc).
All labeling reactions were done in the presence of 200 ng poly-A mRNA
from either human brain or heart.
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Download processed dataset corresponding to print 1 (ZIP archive).
Download processed dataset corresponding to print 2 (ZIP archive).
Download text file containing the location of the yeast controls.
Download MS-EXCEL containing the masses (in picograms) of
the spiked-in yeast RNA.
Download collection of files that contain element
physical locations (subarray/row/column) (ZIP archive).
Examine a listing of the image and processed files available for
the
batch1 and
batch2 collection of experiments.
Download ZIP archive of image files in TIFF format that correspond to
batch1 and
batch2 of the individual experiments.
Download ZIP archive of processed files in TAB-delimited format that
correspond to
batch1 and
batch2 of the individual experiments.
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