Reference Materials
Application Notes
- Image quantitation and flagging for CodeLink Bioarrays
The CodeLink™ Bioarray System includes software for quantitative image data extraction. This
application note provides detailed descriptions of the image quantitation and spot flagging methodologies, and the data export fields employed by the CodeLink Expression
Analysis software (versions 3 through 5).
- CodeLink Bioarray image threshold flagging procedure when using the Agilent G2565BA scanner
Signal strength was found to be different on the Agilent
G2565BA scanner from that on the Molecular Devices GenePix™ 4000B scanner, making it necessary to adjust the threshold accordingly. It was determined that a signal
strength of 1.25 on the G2565BA scanner is equivalent to a signal strength of 1.00 on the GenePix 4000B scanner.
- Scanning CodeLink Bioarrays on GenePix 4000B Array Scanner
This application note describes a recommended scanning procedure and settings on GenePix 4000B Array Scanner for use with CodeLink Bioarrays.
- Scanning CodeLink Bioarrays on Agilent G2565 microarray scanner
This application note describes recommended scanning procedures and settings on Agilent G2565AA and G2565BA scanners for use with CodeLink Bioarrays.
- Spot morphology and its affect on data accuracy and reliability
This application note discusses the spot morphology in Piezo non-contact spotted arrays produced on the CodeLink Activated Slides, and the affect of the spot morphology
on final data output.
- External RNA controls for monitoring performance of CodeLink Whole Genome bioarrays
Here we describe two methods in which the CodeLink Whole Genome control probes can be utilized to generate on-slide controls for sensitivity and dynamic range. In the
first method, individually labeled cRNAs corresponding to the bacterial probes can be spiked into complex background cRNA samples. Results obtained using this method
more accurately reflect bioarray performance because they are independent of RNA starting material and purity; this robustness makes the method ideal for assessing a
within-slide dynamic range of bioarray process, excluding target preparation.
In the second method, each individual bacterial mRNA is spiked at different concentrations into either total or polyA(+) mRNA samples. The signal intensities obtained
for each spike can then be measured, providing a way to assess target preparation efficacy in conjunction with overall microarray performance at each transcript level.
In addition to providing dilutions and spiking procedures for both methods, this application note describes the use of CodeLink Whole Genome control probes in evaluating bioarray sensitivity and dynamic range.
- Improved methodology for assessing the lower limit of detection
This note describes the method for estimating local background noise employed in CodeLink Expression Analysis v4.0 and v5.0 software, which offers improved accuracy
over the global negative-control threshold method used in CodeLink Expression Analysis v2.3.
- Rinse and post-scan re-rinse protocol for background improvement
This application note presents data that demonstrates the improvement obtained with this new rinse protocol, while verifying the back-compatibility of data produced by
the new method.
The note also describes the use of the new rinse protocol for post-scan re-rinsing as a suggested method for eliminating certain high background contaminants that can be
visible during scanning.
Data Files
Scientific Posters
Published Articles
- Evaluation of gene expression measurements from commercial microarray platforms, Nucleic Acids Research 31(19): 5676-5684 (2003).
- Kriete, A. et al. Combined histomorphometric and gene-expression profiling applied to toxicology. Genome Biology, 4:R32 (2003).
- Dorris, D. R. et al. Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios. BMC Biotechnology, 3:6 (2003).
- A 3.9-Centimorgan-Resolution Human Single-Nucleotide Polymorphism Linkage Map and Screening Set, The American Journal of Human Genetics 73. The American Journal of Human Genetics, 73:271-284, (2003).
- Dysregulation of Gene Expression in the 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Lesioned Mouse Substantia Nigrawas, The Journal of Neuroscience, 24(34):7445-7454 + 7445 (2004).
- Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 5:61 doi:10.1186/1471-2164-5-61 (2004)
- Comprehensive comparison of six microarray technologies, Nucleic Acids Research 32(15) e12,doi:10.1093/nar/gnh123 (2004).
- Spatiotemporal patterns of gene expression during fetal monkey brain development, Developmental Brain Research 146: 99-106 (2003).
- Endophyte-Infected Tall Fescue Diet Alters Gene Expression in Heifer Luteal Tissue as Revealed by Interspecies Microarray Analysis Molecular Reproduction and Development 67:154-161 (2004).
