1. Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis
Wanhui You, Stephane Pien, and Ueli Grossniklaus
2. Chromatin Conformation Capture-Based Analysis of Nuclear Architecture
Stefan Grob and Ueli Grossniklaus
3. Metaanalysis of Genome-Wide Chromatin Data
Julia Engelhorn and Franziska Turck
4. Localization of Mirnas by In Situ Hybridization in Plants using Conventional Oligonucleotide Probes
Sara Hernandez-Castellano, Geovanny I. Nic-Can, Clelia De-La-Pena
5. COBRA (Combined Bisulfite Restriction Analysis) Assay for the Analysis of Locus-Specific Changes in Methylation Patterns
Andriy Bilichak and Igor Kovalchuk
6. Analysis of Global Genome Methylation Using the Cytosine-Extension Assay
Andriy Bilichak and Igor Kovalchuk
7. In Situ Analysis Of DNA Methylation in Plants
Palak Kathiria and Igor Kovalchuk
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8. Analysis of DNA Hydroxymethylation in Arabidopsis Using Colorimetric Assay
Andrey Golubov and Igor Kovalchuk
9. Analysis of DNA Cytosine Methylation Patterns using Methylation Specific Amplification Polymorphism (MSAP)
Maria Angeles Guevara, Nuria De Maria, Enrique Saez-Laguna, Maria Dolores Velez, Maria Teresa Cervera, and Jose Antonio Cabezas
10. Differentially Methylated Region - Representational Difference Analysis (DMR-RDA): A Powerful Method to Identify Dmrs in Uncharacterized Genomes
Pavlina Sasheva Ueli Grossniklaus
11. Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays
Martine Boccara, Alexis Sarazin, Bernard Billoud, Agnes Bulski, Louise Chapell, David Baulcombe, and Vincent Colot
12. Northern Blotting Techniques for Small RNAs
Todd Blevins
13. Stem-Loop QRT-PCR for the Detection of Plant Micrornas
Erika Varkonyi-Gasic
14. Profiling New Small RNA Sequences
Masayuki Tsuzuki and Yuichiro Watanabe
15. Small RNA Library Preparation and Illumina Sequencing in Plants
Andriy Bilichak, Andrey Golubov, and Igor Kovalchuk
16. Bioinformatics Analysis of Small RNA Transcriptomes - The Detailed Work Flow<
Slava Ilnytskyy and Andriy Bilichak
17. Increasing a Stable Transformation Efficiency of Arabidopsis by Manipulating the Endogenous Gene Expression using Virus-Induced Gene Silencing
Andriy Bilichak and Igor Kovalchuk
18. The Random Oligonucleotide-Primed Synthesis Assay for the Quantification of DNA Strand Breaks
Andriy Bilichak and Igor Kovalchuk
19. Profiling Transposable Elements and their Epigenetic Effects in Non-Model Species
Christian Parisod
