Links
Software Resources
R and Bioconductor: Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data using the R statistical package. From this site you can access R, the bioconductor analytic packages, and get additional information and documentation.
Microarrays: A public resource created and maintained by the DeRisi lab at UCSF, for microarray protocols and software. Many good links within.
BRB Array Tools An integrated package for the visualization and statistical analysis of DNA microarray gene expression data.
DAVID and EASE Free NCBI software for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms.
MIAME This site describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment; most journals will require data to be submitted in this format.
This is not a comprehensive list but is just meant to get you started. If you find any other particularly useful links please let us know and we'll update our list.
Protocols
RNA labeling 1 (facility derived)
RNA labeling 2 (DeRisi lab derived)
These protocols are intended to give you a basic idea of how some of these techniques are done. As with any lab manipulations these protocols are representative of an evolving methodology, and should not necessarily be seen as set-in-stone endpoints. It's always a good idea to talk with people routinely doing these experiments to get the best tips and insight.
Other Sites of Interest
Chip on chip.org This site, hosted by Bing Ren's lab at UCSD, is an excellent resource for information about primary antibodies that have been shown to work in chromatin immunoprecipitation. Researchers can scan a number of commercial antibodies to see if they've been deemed chIP-worthy. Input from researchers doing immunoprecipitations is solicited, making this database a constantly evolving resource.