Processing ChIP-chip data: from the scanner to the browser

Microarray experiments and factors which affect their reliability

Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very complex, requiring sophisticated methods to control for various factors that are inherent to the procedures used. In this article we describe the individual steps of a microarray experiment, highlighting important elements and factors that may affect the processes involved and that influence the interpretation of the results. Additionally, we describe methods that can be used to estimate the influence of these factors, and to control the way in which they affect the expression estimates. A comprehensive understanding of the experimental protocol used in a microarray experiment aids the interpretation of the obtained results. By describing known factors which affect expression estimates this article provides guidelines for appropriate quality control and pre-processing of the data, additionally applicable to other transcriptome analysis methods that utilize similar sample handling protocols.

Genome-wide analysis of transcription factor-binding sites in skeletal muscle cells using ChIP-seq

Transcriptional regulation of gene expression constitutes a fundamental mechanism of many developmental processes. Therefore, identification and characterization of binding sites of transcription factors are important for uncovering the mechanisms of a particular developmental process. Here, we describe detailed procedures for genome-wide analysis of binding sites of a transcription factor involved in the fiber-type differentiation of skeletal muscle. By conducting ChIP-seq followed by a series of downstream analyses, in-depth information on binding sites of transcription factors can be obtained in a genome-wide manner.