Part I. Growing Arabidopsis

1. Handling Arabidopsis Plants: Growth, Preservation of Seeds, Transformation and Genetic Crosses

Luz Rivero, Randy Scholl, Nicholas Holomuzki, Deborah Crist, Erich Grotewold, and Jelena Brkljacic

2. Using Arabidopsis Related Model Species (ARMS): Growth, Genetic Transformation and Comparative Genomics

Giorgia Batelli, Dong-Ha Oh, Matilde Paino D'Urzo, Francesco Orsini, Maheshi Dassanayake, Jian-Kang Zhu, Hans J. Bohnert, Ray A. Bressan and Albino Maggio

3. Growing Arabidopsis in vitro: Cell Suspensions, in vitro Culture, and Regeneration

Bronwyn J. Barkla, Rosario Vera-Estrella, and Omar Pantoja

Part II. Arabidopsis resources

4. Arabidopsis Database and Stock Resources

Donghui Li, Kate Dreher, Emma Knee, Jelena Brkljacic, Erich Grotewold, Tanya Z. Berardini, Philippe Lamesch, Margarita Garcia-Hernandez, Leonore Reiser and Eva Huala

5. Bioinformatic Tools in Arabidopsis Research

Miguel de Lucas, Nicholas J. Provart, and Siobhan Brady

Part III. Genetic techniques

6. Exploiting Natural Variation in Arabidopsis

Johanna A. Molenaar and Joost J. B. Keurentjes

7. Grafting in Arabidopsis

Katherine Bainbridge, Tom Bennett, Peter Crisp, Ottoline Leyser, and Colin Turnbull

8. Agrobacterium tumefaciens Mediated Transient Transformation of Arabidopsis thaliana Leaves

Silvina Mangano, Cintia Daniela González, and Silvana Petruccelli

9. iTilling: Personalized Mutation Screen

Susan M. Bush and Patrick J. Krysan

10. Tailor Made Mutations in Arabidopsis Using Zinc-Finger Nucleases

Yiping Qi, Colby G. Starker, Feng Zhang, Nicholas J. Baltes, and Daniel F. Voytas

11. The Use of Artificial Micro RNA Technology to Control Gene Expression in Arabidopsis thaliana

Andrew L. Eamens, Marcus McHale, and Peter M. Waterhouse

12. Generation and Identification of Arabidopsis EMS Mutants

Li-Jia Qu and Gengi Qin

13. Generation and Identification of Arabidopsis T-DNA Insertion Mutants

Li-Jia Qu and Gengi Qin

14. Identification of EMS-induced Causal Mutations in Arabidopsis thaliana by Next-Generation Sequencing

Naoyuki Uchida, Tomoaki Sakamoto, Masao Tasaka, and Tetsuya Kurata

15. Arabidopsis Transformation with Large Bacterial Artificial Chromosomes

Jose M. Alonso and Anna N. Stepanova

16. Global DNA Methylation Analysis Using Methyl-Sensitive Amplification Polymorphism (MSAP)

Mahmoud W. Yaish, Mingsheng Peng, and Steven J. Rothstein

Part IV. Molecular biological techniques

17. Next Generation Mapping of Genetic Mutations Using Bulk Population Sequencing

Ryan S. Austin, Steven P. Chatfield, Darrell Desveaux, and David S. Guttman

18. Chemical Fingerprinting of Arabidopsis Using Fourier-transform Infrared (FT-IR) Spectroscopic Approaches

András Gorzsás and Björn Sundberg

19. A Pipeline for 15N Metabolic Labeling and Phosphoproteome Analysis in Arabidopsis thaliana

Benjamin B. Minkoff, Heather L. Burch, and Michael R. Sussman

20. Gene Expression Profiling Using DNA Microarrays

Kionoshin Maruyama, Kazuko Yamaguchi-Shinozaki, and Kazuo Shinozaki

21. Forward Chemical Genetic Screening

Hyunmo Choi, Jun-Young Kim, Young Tae Chang, and Hong Gil Nam

22. Highly-Reproducible ChIP-On-Chip Analysis to Identify Genome-Wide Protein Binding and Chromatin Status in Arabidopsis thaliana

Jong-Myong Kim, Taiko Kim To, Maho Tanaka, Takaho A. Endo, Akihiro Matsui, Junko Ishida, Fiona C. Robertson, Tetsuro Toyoda, and Motoaki Seki

Part V. Cell biological techniques

23. Fluorescence Microscopy

Sebastien Peter, Klaus Harter