1. Circadian Rhythm: Phase Response Curve and Light Entrainment
Xiaodong Xu, Li Yuan, and Qiguang Xie
2. Period Estimation and Rhythm Detection in Timeseries Data Using BioDare2, the Free, Online, Community Resource
Tomasz Zieliński, Johnny Hay, and Andrew J. Millar
3. Detection and Analysis of Circadian Rhythms Via Prompt Chlorophyll Fluorescence
Yuri Dakhiya and Rachel Green
4. High Spatial Resolution Luciferase Imaging of the Arabidopsis thaliana Circadian Clock
Mark Greenwood, Anthony J.W. Hall, and James C.W. Locke
5. Agrobacterium-mediated seedling transformation to measure circadian rhythms in Arabidopsis
Michael K. Y. Ting, Reimo Zoschke, and Michael J. Haydon
6. Measurement of Luciferase Rhythms in Soybean Hairy Roots
Qiguang Xie, Yu Wang, Li Yuan, and Xiaodong Xu
7. ODE (ordinary differential equation) Models for Plant Circadian Networks: What The Models Are, and How They Should Be Used
Jonathan W. Pitchford and Paula Avello Fernandez
8. How to Detect QTLs in the Plant Circadian Clock
Muhammad Usman Anwer and Marcel Quint
9. Measuring Hypocotyl Length in Arabidopsis
James Ronald and Seth J. Davis
10. High Throughput Extraction and Enzymatic Determination of Sugars and Fructans In Fructan-Accumulating Plants
Kallyne A. Barros, Masami Inaba, Auxiliadora Oliveira Martins, and Ronan Sulpice
11. Simple Nuclei Preparation and Co-Immunoprecipitation Procedures for Studying Protein Abundance and Interactions In Plant Circadian Time Courses
Akane Kubota, Young Hun Song, and Takato Imaizumi
12. Chromatin Immunoprecipitation Protocol for Circadian Clock Proteins
Sally Adams and Isabelle A. Carr
13. A high-throughput 3′-Tag RNA Sequencing for Large-Scale Time-Series Transcriptome Studies
Xiaoyu Weng and Thomas E. Juenger
14. Experimental Design for Time-Series RNA-seq Analysis of Gene Expression and Alternative Splicing
Nikoleta A. Tzioutziou, Allan B. James, Wenbin Guo, Cristiane P. G. Calixto, Runxuan Zhang, Hugh G. Nimmo, and John W. S. Brown
15. Using tandem affinity purification to identify circadian clock protein complexes from Arabidopsis
Maria L. Sorkin and Dmitri A. Nusinow
16. Firefly Luciferase Complementation-Based Analysis of Dynamic Protein-Protein Interactions under Diurnal and Circadian Conditions in Arabidopsis
Qiguang Xie, Qiao Wang, and Xiaodong Xu
17. Monitoring Seasonal Bud Set, Bud Burst, and Cold Hardiness in Populus
Mikael Johansson, Naoki Takata, Cristian Ib ez, and Maria E. Eriksson
18. The Perennial Clock Is an Essential Timer for Seasonal Growth Events and Cold Hardiness
Mikael Johansson, Cristian Ib ez, Naoki Takata, and Maria E. Eriksson