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These protocols were largely derived from the Cold Spring Harbor Laboratory Microarray Course manual. Contributors include: H.Bennett, J. DeRisi, V.Iyer, M. Diehn, A. Alizadeh, J.Lieb, and other members of the Brown and DeRisi labs.

Call for Protocols:

This is public place for protocol distribution. If you have a protocol that you think would be of use to the microarray community, please



The Process - June 2001
Provides a simple overview of the microarray process.

Slide Preparation

Preparation of Poly-l-Lysine Slides - June 2001
Directions for cleaning and coating slides with poly-l-lysine.

Directions for Printing Arrays

Instructions for Printing Arrays - June 2000
Directions for print run initiation through completion.

DNA Preparation

Random DNA Amplification - June 2001
Directions for amplifying products for printing on arrays.
cDNA Clone Preparation - June 2000
Protocol for preparation of plasmid DNA containing mammalian cDNA clone.
DNA Precipitation - June 2000
Protocol for precipitating DNA in 96 well plates and transfer to 384 printing plates.

Tips and Tricks

Yeast Expression Analysis - June 2001
Tips and pointers for designing yeast expression experiments.

Yeast Farming - June 2001
Sean O'Rourke's famous yeast farming guide for expression experiments.

Nucleic Acid Preparation

E.coli Total RNA Isolation - October 2000
Protocol for isolation of E.coli total RNA from the Gross Lab.
Yeast Total RNA Isolation - June 2001
Protocol for isolation of yeast total RNA by the hot acid phenol method.
Yeast Poly(A)+ mRNA Isolation - June 2001
Protocol for isolation of yeast poly(A)+ mRNA by the oligo-dT cellulose method.
Human FastTrack mRNA Isolation
Revised protocol for FastTrack 2.0 mRNA extraction from human cells
Human Tumor mRNA Isolation - June 2000
Protocol for extraction of mRNA from human tumors.
Membrane Bound Polysome Isolation - June 2001
Protcol for extraction of mRNA associated with membrane bound polysomes via the gradient method.
Yeast ChIP-on-Chip - June 2001
Protocol for isolation of DNA associated with DNA binding proteins by crosslinking and subsequent immunoprecipitation.

Nucleic Acid Labeling

Reverse Transcription and aa-UTP Labeling of RNA - June 2001
Protocol for making cDNA with aa-dUTP incorporation and labeling cDNA via chemical coupling of fluorescent dyes.
Reverse Transcription and Labeling of Human RNA - June 2000
Protocol for direct incorporation of fluorescent nucleotides into cDNA reverse transcribed from human mRNA.
Modified Eberwine RNA Amplification - June 2000
Protocol for amplifying RNA using a modified "ANTISENSE"(Eberwine) method.
Labeling Genomic DNA Version A - June 2000
Labeling Genomic DNA Version B
Protocols for labeling genomic DNA via direct incorporation or coupling for comparative genomic hybridizations.
Amplification and Labeling of DNA - June 2000
Protocol for amplifying and labeling DNA from ChIP or elsewhere.

Array Post Processing

Post Processing Array - June 2001
Instructions for hydrating and fixing spotted DNA and chemically blocking the poly-l-lysine surface.

Array Hybridization

Array Hybridization - June 2001
Protocol describing hybridization set up and probe application.
Array Washing - June 2001
Instructions for washing microarrays after hybridization.

Scanning Microarrays

Array Scanning - June 2000
An introduction to the Axon GenePix 4000a Microarray Scanner.


Supply Source Sheet - June 2000
A comprehensive list of the supplies you need to run many of the protocols described above.