Dunham Lab Protocols


Dr. Maitreya Dunham, Lewis-Sigler Fellow

Lewis-Sigler Institute for Integrative Genomics

Carl Icahn Laboratory, Princeton University




Dunham Lab Protocols


Almost all the microarray protocols have been updated, either to accommodate Agilent's latest randomization of their reagents or to circumvent recurring artifacts (the CGH protocol in particular). Please note that I didn't cut these protocols from whole cloth. They are mostly derived from the work of others, plus my own amendments and annotations.


Chemostat Protocols

Microarray Protocols


Protocols are specifically for yeast, but they also work for other species. Also, the Agilent protocols are for 4x44k arrays, but it turns out all that needs adjusted for the different platforms is the volume, not the amount of labeled material. Check the Agilent manuals for recommended volumes.

  • Ozone and Cy5 [HTML]

  • Agilent arrays: RNA [HTML][PDF]

  • Agilent arrays: DNA [HTML][PDF]

  • Agilent arrays: PFGE bands [HTML][PDF]

  • Agilent arrays: transposon mapping [HTML][PDF]

  • Agilent arrays: PUMA [HTML][PDF]

  • Agilent arrays: stripping [HTML][PDF]

  • Homemade arrays: RNA [HTML][PDF]

  • Homemade arrays: DNA [HTML][PDF]

  • Homemade arrays: PUMA [HTML][PDF]

Genotyping Protocols

  • Genomic mismatch scanning [HTML][PDF]

  • Affymetrix arrays: DNA [HTML][PDF]

Yeasty Protocols

  • yeast RNA prep [HTML][PDF]

  • yeast DNA prep [HTML][PDF]

  • yeast mating type halo assay [HTML][PDF]

  • Comparison of a bunch of yeast minimal media supplements [HTML][PDF]

  • Yeast minimal media supplements inherited from the Botstein lab [HTML][PDF]

  • Yeast lithium acetate transformation [HTML][PDF]

  • Yeast sporulation and dissection [HTML][PDF]