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Protocols 

Almost all the microarray protocols have been updated, either to accomodate 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

New Chemostat Manual for a cheap array of small volume chemostats, or "ministats" [PDF][Appendix of supplies]

Chemostat Manual for use with glass-blown fermenters [HTML][PDF]

Old Chemostat Manual for use with ATR Sixfors fermenters [HTML][PDF]

Phosphate assay [HTML][PDF]

Glucose assay [HTML][PDF]

Ethanol assay [HTML][PDF]

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]

questions?

Email me (maitreya [at] uw [dot] edu) if you have any questions or additions.

I (or the person who I got the protocol from, as indicated) would also appreciate the citation if you use any of these protocols.


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