Includes bibliographical references and index.

Analysis of DNA methylation in plants by bisulfite sequencing / Andrea Foerster and Ortrun Mittelsten Scheid -- Analysis of bisulfite sequencing data from plant DNA using CyMATE / Andrea M. Foerster ...[et al.] -- Analysis of locus-specific changes in methylation patterns using a COBRA (combined bisulfite restriction analysis) assay / Alex Boyko and Igor Kovalchuk -- Detection of changes in global genome methylation using the cytosine-extension assay / Alex Boyko and Igor Kovalchuk -- In situ analysis of DNA methylation in plants / Palak Kathiria and Igor Kovalchuk -- Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism / Alex Boyko and Igor Kovalchuk -- Isoschizomers and amplified fragment length polymorphism for the detection of specific cytosine methylation changes / Leonor Ruiz-García ... [et al.] -- Analysis of small RNA populations using hybridization to DNA tiling arrays / Martine Boccara ... [et al.] -- Northern blotting techniques for small RNAs / Todd Blevins -- qRT-PCR of small RNAs / Erika Varkonyi-Gasic and Roger P. Hellens -- Cloning new small RNA sequences / Yuko Tagami, Naoko Inaba, and Yuichiro Watanabe -- Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitatino and DNA microarray hybridization (ChIP-chip). Part A : ChiP-chip molecular methods / Julia J. Reimer and Franziska Turck. Part B : ChIP-chip data analysis / Ulrike Göbel, Julia Reimer, and Franziska Turck -- Metaanalysis of ChIP-chip data / Julia Engelhorn and Franziska Turck -- Chromatin immunoprecipitation protocol for histone modifications and protein-DNA binding analyses in Arabidopsis / Stéphane Pien and Ueli Grossniklaus -- cDNA libraries for virus-induced gene silencing / Andrea T. Todd, Enwu Liu, and Jonathan E. Page -- Detection and quantification of DNA strand breaks using the ROPS (random oligonucleotide primed synthesis) assay / Alex Boyko and Igor Kovalchuk -- Reporter gene-based recombination lines for studies of genome stability / Palak Kathiria and Igor Kovalchuk -- Plant transgenesis / Alicja Ziemienowicz.