Direct labeling of mouse genomic DNA for microarray hybridization using the Klenow fragment of E. coli DNA polymerase I and Cy3 dCTP. - Version 1.0, December 29, 2003
Brian Williams & Richele Gwirtz
This is a detailed version of the protocol published in .Genomic DNA as a cohybridization standard for mammalian microarray measurements., Brian A. Williams, Richele M. Gwirtz and Barbara J. Wold. Nucleic Acids Research, 2004, Vol. 32, No. 10, e81.
This protocol is designed to produce a cohybridization standard for use on microarrays that represent genomes with relatively low gene density (such as the mouse genome). To effectively label a single array with this standard, 3 aliquots (2 .gs each) of sonicated mouse genomic DNA (see our associated protocol for preparing mouse genomic DNA) should be labeled as described below. These can then be combined for cohybridization with a single, labeled cDNA sample.
Indirect labeling of mouse genomic DNA using Klenow and aminoallyl-dUTP - Version 1.0, October 7, 2004
Brian Williams & Richele Gwirtz
This is a detailed version of the protocol published in .Genomic DNA as a general cohybridization standard for ratiometric microarrays., Brian A. Williams, Richele M. Gwirtz and Barbara J. Wold. Methods in Enzymology, (2006) DNA microarrays Part A: Array platforms and wet-bench protocols, volume 410, chapter 14.
This protocol is designed to produce a cohybridization standard for use on microarrays that represent genomes with relatively low gene density (such as the mouse genome). To effectively label a single array with this standard, 3 aliquots (2 .gs each) of sonicated mouse genomic DNA (see our associated protocol for preparing mouse genomic DNA) should be labeled as described below. These can then be combined for cohybridization with a single, labeled cDNA sample.
Preparing Mouse Genomic DNA using the EPICENTRE MasterPure complete DNA purification kit - Version 1.0, May 14 2004
Brian Williams & Richele Gwirtz
This protocol is taken from the publication: .Genomic DNA as a general cohybridization standard for ratiometric microarrays., Brian A. Williams, Richele M. Gwirtz and Barbara J. Wold. Methods in Enzymology, (2006) DNA microarrays Part A: Array platforms and wet-bench protocols, volume 410, chapter 14.
Label incorporation and yield of target are strongly influenced by the source of genomic DNA used as template. In our hands, genomic DNA from several commercial suppliers gave inefficient labeling compared with companion reactions using DNA prepared directly from mouse tissue. This method allows specification of the strain, genotype and sex of the genomic DNA standard, thereby allowing the evaluation of qualitative differences in Y-linked genes, and quantitative differences in X-linked genes.