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
