instrument was developed in Pat
Brown's lab in the Biochemistry
We have constructed a two-color
(green and red)
laser-fluorescence-based scanner for scanning a medium-density array of
cDNA probes hybridized onto coated glass slides.
A typical slide contains upto 10000 probes, arrayed in a 1 sq. inch area.
Two-color laser scanning allows quantitative
studies of gene-expression in two samples simultaneously. The two samples
are distinguished thru labeling with the fluorescent dyes Cy3 and Cy5.
The fluorescence signal
is amplified by PMTs and collected by a fast A/D board. A typical scan
takes about 15 minutes and collects about 14 million pixels of 16-bit data
for each channel. The software driving the xy-scan motion control and the
data acquisition board is written in Labview
by National Instruments Corp.. After
data averaging and compression, the data files for each channel are about
1 Mbyte large, at the 16-bit resolution. The data files are compatible
with and are readily analysed by AIS imaging software as well as NIH Image.
A dynamic range of 1000:1 is easily obtained. This value is limited by
background 'biochemical' noise, inherent in the present protocol for slide
The resolution of the scan
in the present system is limited by the laser spot size and is approximately
10-20 microns. The motion control system has a specified resolution of
about 3 microns. Thus, features on the order of 100 microns are easily
resolved by the scanner.
Drawings for this instrument
are available from Pat Brown's