Summary
Abstract
Protocol
Discussion
Materials
References
Biology
Gene microarrays are powerful tools in gene expression profiling at a genome-wide level. This technology has application in a variety of biological disciplines including developmental biology and toxicology. In this video, we detail a protocol for global gene expression analysis using a comprehensive oligonucleotide microarray platform for the zebrafish.
Part 1: Fluorescent Labeling of cDNA
The Cy3 dye used in the microarray experiment is sensitive to photo-degradation. The procedure should take place in a minimal amount of light. The labeling protocol was adapted from the BioPrime Array CGH Genomic Labeling System Manual1.
Many microarray protocols, including the one detailed here, use fluorescent dyes as a means of measuring and quantifying hybridization. The Cy3 fluorescent dye is sensitive to photo and ozone degradation. It is recommended that the procedure be conducted in minimal lighting. In addition, small dust particles can interfere with hybridization and scanning. Special attention should be given to make sure the work area is clean and free from dust.
There are many alternatives to the labeling protoc.......
Material Name | Type | Company | Catalogue Number | Comment |
---|---|---|---|---|
Name | Company | Catalog Number | Comments | |
Array Microcentrifuge Dryer | ISC Bioexpress | C-1303-T | ||
BioPrime Array CGH Genomic Labeling System | Invitrogen | 18095-011 | ||
Cyanine 3-dCTP | PerkinElmer | NEL576 | ||
GenePix 4000B | Molecular Devices | GENEPIX 4000B | ||
Microcon YM-30 | Millipore | 42411 | ||
NimbleGen Array Processing Accessories | Roche NimbleGen | 5223539001 | ||
NimbleGen Hybridization Kit | Roche NimbleGen | 5223474001 | ||
NimbleGen Hybridization System 4 | Roche NimbleGen | 5223652001 | ||
NimbleGen Wash Buffer Kit | Roche NimbleGen | 5223504001 | ||
X1 Mixers | Roche NimbleGen | 5223725001 |
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