Microarray protocols and overviews
(Curr Protoc Mol Biol.)
1: Curr Protoc Mol Biol. 2007 Jan;Chapter 19:Unit 19.6.
Analysis and management of microarray gene expression data.
Grant GR, Manduchi E, Stoeckert CJ Jr.
University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Microarray experiments require careful planning and choice of analysis tools in
order to get the most out of the data generated, especially considering the
associated significant cost and effort. Microarray experiments also require
careful documentation, often residing in local databases and/or submitted to
public repositories. An often bewildering assortment of choices is available for
experimental design, data preprocessing, data analysis (e.g., differential gene
expression, classification), and data management. This unit covers the basic
steps and common applications for planning, data processing, and data management
of microarray experiments, and provides guidance to making choices based on the
goals and practical realities of the experiment, as well as the authors'
experience in this area.
2: Curr Protoc Mol Biol. 2004 Sep;Chapter 22:Unit 22.4.
Overview of mRNA expression profiling using microarrays.
Katagiri F, Glazebrook J.
University of Minnesota, St. Paul, Minnesota, USA.
Microarray technology allows simultaneous measurement of the mRNA levels of
thousands of genes. This powerful technology has applications in addressing many
biological questions that were not approachable previously; however, the enormous
size of microarray data sets leads to issues of experimental design and
statistical analysis that are unfamiliar to many molecular biologists. The type
of array used, design of the biological experiment, number of experimental
replicates, and statistical method for data analysis should all be chosen based
on the scientific goals of the investigator. This overview presents a discussion
of the relative merits and limitations of various methods with respect to some
common applications of microarray experiments.
3: Curr Protoc Mol Biol. 2004 Nov;Chapter 21:Unit 21.9.
Defining in vivo targets of nuclear proteins by chromatin immunoprecipitation and
Moqtaderi Z, Struhl K.
Harvard Medical School, Boston, Massachusetts, USA.
This unit describes the combination of chromatin immunoprecipitation (ChIP) with
microarray hybridization to determine the genome-wide occupancy profile of a
DNA-associated protein. After conventional ChIP, the immunoprecipitated material
is amplified by a two-step process involving primer extension followed by PCR in
the presence of a modified nucleotide. The amplified DNA is fluorescently labeled
in a reaction that couples dye to the modified nucleotide, and the labeled sample
is hybridized to a microarray representing a complete genome. This method allows
the study of a protein's pattern of DNA association across an entire genome with
no need for prior knowledge of potential DNA targets.
Bead arrays technology (NCBI)
ProbeDB > Technologies > Bead Arrays
Microarray books (Biowww bookshelf)
microarray technique and analysis