Journal:

Article Title: Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays

doi:

Figure Lengend Snippet: Hyperspectral scan results of a hybridized Corning preprinted array showing contaminating fluorescence in the presence of Cy3. Regions of a Cy3- and Cy5-cDNA hybridized Corning preprinted DNA microarray were scanned with both the hyperspectral imaging and the Axon 4000B scanners at 10 µm spatial resolution. The spectra and concentration maps were generated from multivariate image analysis of hyperspectral images containing 46800 spectra from a 3.9 × 2.3 mm area. Each image is scaled proportional to the total intensity of the Axon 4000B ratio image for visual comparison. The appropriate scale factors were calculated by multiplying each spectrum times its concentration map and applying a filter function similar to the optical filter used on the commercial scanner (Axon). (A) Emission spectra of fluorescent species, normalized to unit length. These fluorescent emissions would all be confounded in the green channel of commercial microarray scanners. (B) Corresponding concentration maps of fluorescent species. (C) Ratio image of same area of the same slide collected on an Axon 4000B scanner and visualized with GenePix Pro.

Article Snippet: Scanning and data analysis Hyperspectral imaging data were collected on one Corning preprinted DNA microarray that had been hybridized with Cy3- and Cy5-labeled cDNA synthesized from 20 µg of yeast RNA.

Techniques: Fluorescence, Microarray, Imaging, Concentration Assay, Generated

Journal:

Article Title: Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays

doi:

Figure Lengend Snippet: Contaminating fluorescence after hybridization cannot be accurately predicted by pre-hybridization scans. Spots from a commercial microarray slide (CMT12015426, lot 28300001, Corning) were quantified before and after mock-hybridization. Spot intensity was calculated as (median pixel intensity – median background pixel intensity) for the green channel (532 nm). Percent loss of contaminating fluorescence was calculated as [1 – (spot intensity after treatment/spot intensity before treatment)] × 100%. The spot intensity before treatment was graphed relative to the % loss of contaminating fluorescence. Only those spots with intensities >500 (after background subtraction), for the green channel before treatment, were included in this graph (n = 3933).

Article Snippet: Scanning and data analysis Hyperspectral imaging data were collected on one Corning preprinted DNA microarray that had been hybridized with Cy3- and Cy5-labeled cDNA synthesized from 20 µg of yeast RNA.

Techniques: Fluorescence, Hybridization, Microarray